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Update Feb 20, 2015:
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As many games are only available in their home language of Japanese you may or may not have trouble getting through them without some sort of guidance. That's where the following programs will assist. 
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USE VNR FOR EVERYTHING. this guide is outdated, VNR has made some pretty big steps into improving jp to eng machine translation and the changes have been really big. Disregard everything in this guide about chiitrans lite, shit sucks now, VNR has updates like almost every day improving machine translation. Update this guide when I can. But basically use VNR for everything, the best translators still are
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Atlas with errzotl's dictionary + TAH script > LEC offline translator (torrent power translator 15) + TAH script >>> honyaku/infoseek/excite (all similar it seems like variations of LEC) = google >>>>>>>> bing
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Programs marked with a * require usage of hook codes. Despite build-in text thread detection, some games make grabbing text from them more difficult than others due to the way they've been coded and that's where these mythical hook codes help programs get them right. You can find some of these in relevant pastebins, or just googling for something like "gamename agth ith h-code". The agthDB is dead now 
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I'll update the guide when I'm not lazy.
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>Offline Translators 
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June 8th-2015: holy shit im lazy.
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Download: <https://mega.nz/#!6pJX0QzI!ZaE1lrK7VmDUuymC0iAKzas2iNFRTGH6BXDjOdAcj_o>
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Intro:
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This archive contains both Atlas and LEC. Follow directions for setting up your offline translators, link them with your translation environment, and never rely on Google or Bing again. Make sure to set your date back before 2009 to install the trial 
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This is my own personal setup, I don't consider myself an expert on this, for all I know I might be doing it wrong. But it works for me as well as a few anons. Also before following this know you can just use VNR by itself since it contains everything in a neat package, these extra steps and programs are just for getting a better and more coherent machine translation, also autism.
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/hgg/ Machine Translation Guide: https://pastebin.com/i6k9krCP 
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General Settings and setup - http://a.pomf.se/sspvsp.PNG
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**RPG maker MV games require you to patch with the MV patch in order to MTL** 
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How it looks like in the end - http://a.pomf.se/zyzodq.PNG
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**New wolfRPG games require an individual hook code to MTL** 
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The Programs I use:
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>Chiitrans lite 
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VNR (Visual Novel Reader):
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http://sakuradite.com/
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Download: <http://alexbft.github.io/chiitrans/ChiitransLite.msi>
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Patch for Google Translate: <https://mega.nz/#!Qm4hBDiS!dIkD17EOpxgjNk0q-OiVnsWUVUCinuex3i-j_bp6G_0>
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Chiitrans Lite:
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Replace translators.js and translators.coffee in "{Install location}\Chiitrans Lite\www\js" with the files in the zip to enable google translate. Once installed, Open chiitrans lite and click "Options" Make sure "Capture text from Clipboard" is checked and then click on translation. Choose whether you want to see source only (Japanese), translations only (English)[recommended] or both at the same time. Click on additional translators and choose the ones you want to use (recommended Google and/or Atlas). Click OK, then OK again to save your settings. While the game is running, choose the process from the dropdown (usually game.exe), open the .exe file using the folder button or select the window with the window button and click connect. The game should now be translated in the translation window as you play. 
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https://alexbft.github.io/chiitrans/
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If you are getting a blank box when hooking with chiitrans lite, then use ITH VNR as a workaround:
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Atlas V14:
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Download: <http://www.mediafire.com/download/8zjhfxys78r0bfs/ITHVNR-3.5640.1-win32.zip>
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Download and Installation Guide (Only follow the "Installing Atlas" section):
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Mirror: <https://mega.nz/#!UrRDxQjL!dkhAmM6MgMgDJ1V7QWAEnpoVKT27uc2ug9rro0A9sDk>
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https://amaenboda.wordpress.com/2012/03/26/an-aero-gamers-guide-to-using-atlas/3/#Installing%20ATLAS
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mirror of the link above - http://pastebin.com/vWpmFGK9
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>Visual Novel Reader 
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Alternative download (Just in case, also this torrent is a bit outdated since I believe its using an older update so use the one above if you can):
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http://www.nyaa.se/?page=view&tid=89984
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Download: <https://mega.nz/#!YJBzlZyS!77xahQf-LiUOX1ZAS4y9yAXBkHyyDSuTeYGunwWj9X4>
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Errzotl's Atlas Dictionary:
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**This program is not suggested if you doubt your computers performance or are concerned about space**
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http://www.hongfire.com/forum/showthread.php/94395-Translation-Aggregator-v0-4-9?p=2269439#post2269439
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**Development on VNR has ceased, No longer recommended since it's obsolete bloatware now.**
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I only download the "Atlas dictionary 2014 rev 01", Instructions on how to install are inside. Don't need to download the TAH scripts since both VNR and Chiitrans Lite already come with them. Errzotl's work greatly improves the machine translation of Atlas.
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>Translation Aggregator* 
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Info:
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VNR i use for text hooking (capturing the text/dialogue) and Chiitrans lite for translating. I do this because even though VNR can translate as well, I get better translations with Chiitrans lite. On the other hand, Chiitrans Lite can also text hook but the text hooking is currently better in VNR since it can text hook a wider variety of VNs and the like (for example Tinklebell's Rondo Duo).
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Info: <http://www.hongfire.com/forum/showthread.php/94395-Translation-Aggregator-v0-4-9>
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Download with a portable version of LEC pre-installed with the Edict file from 21/10/2017: 
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I'm not entirely sure as to why VNR's Atlas translation and Chiitran Lite's Atlas translation are different despite using the same translator. I'm guessing it's because VNR doesnt use the proper Atlas Environment while Chiitrans does. It is for this reason that I use Chiitrans for translating, VNR's atlas translation will sometimes give you romaji and gibberish as if it doesnt know the word that it's translating, also I've found in VNR's Atlas with VNs like Rondo Duo you get messed up text and symbols in weird places.
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<https://mega.nz/#!8mxhTKAB!lsK_a1a5euggBW9VhC5d72nyYMZUKY_SpN60_tvEYQc>
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Download for version with working Google Translator:
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Guide
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<http://www.hongfire.com/forum/forum/hentai-lair/hentai-game-discussion/tools-and-tutorials/68499-translation-aggregator/page44#post6088463>
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1. Install everything listed on The Programs I use, follow the instructions there. don't mess up installing Atlas and merging the dictionary because that's possible and you might have to reinstall everything again.
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Make sure to uncheck "Translate windows menus with Atlas" in "Additional Options" when hooking or else you will get an error. 
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2. http://a.pomf.se/yhkfsw.JPG
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>Latest Jparser Edict File 
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Start VNR then Chiitrans. Then on Chiitrans Lite options enable errzotl's TAH script. In Chiitrans you do it by going to Options > Translation > Additional Translators and adding "Atlas with TAHelper Replacements", also make sure the Atlas Environment that is used matches the one where you installed Errzotl's dictionary (usually in general).
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(Optional: if using VNR to translate -which I don't but I still have this enabled just because- In VNR you do it by going to your preferences > translation > translators > check Atlas offline machine translation under TAH script for Jap-Eng machine translators.)
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Download: <http://ftp.monash.edu/pub/nihongo/edict2.gz>
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Place edict2.gz in Translation Aggregator's dictionaries folder and delete any other edict files that were in there. 
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3. Run your game, in your in-game settings make sure the text/dialogue speed is set at max (usually its obvious which setting it is. if not, just test settings in game till you get it). VNR should automatically recognize your game. If not add it using VNR's Game Wizard (the 2nd blue button in the spring board), select the process of the game running and if VNR doesnt automatically grab the settings that are needed, you will have to figure out which text thread is the one that has the dialogue on the screen. In the actual VN make sure you're at a part where text/dialogue is shown, skip to next line so VNR attempts to find the dialogue. The default Text encoding (SHIFT-JIS) works for more VNs but for Tinklebell's works that use flash you will have to use UTF-16. If for whatever reason you still can't find the correct text thread, make sure you update your VNR (right click tray icon > check for updates).
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>Interactive Text Hooker* 
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4. http://a.pomf.se/sspvsp.PNG In VNR 
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As shown in the pic, VNR gives you a small menu to the left of your game. If you hover your mouse over the left side, under Option, make sure you enable "Text to clipboard" (I disable Game Text and Machine Translation too since I use Chiitrans). On Chiitrans Lite Options enable "Capture Text from clipboard".
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Wiki: <https://code.google.com/p/interactive-text-hooker/w/list>
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Download: <https://code.google.com/p/interactive-text-hooker/>
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5. On Chiitran Lite's main window click on "TL Window" (Do NOT click on Connect or select your exe/window this is for text hooking in chiitrans which you are already doing with VNR). This is the transparent window that has the actual translation. it will translate whatever japanese text is in your clipboard. You can change the transparency at the top left of this window (click the square) as well as the text size. This is it.
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>Anime Games Text Hooker* 
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*********The order i open my programs is always VNR first. VNR > Game > Chiitrans. VNR > Chiitrans > Game also works. Make sure no other instances of chiitrans is running on your task manager before opening anything. If any of the programs start failing, restart/update.*********
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Manual: <https://sites.google.com/site/agthook/manual>
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Notes:
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Download: <https://sites.google.com/site/agthook/>
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http://a.pomf.se/jjtmna.JPG 
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If you want romaji select latin under the chiitrans lite parsing options and on Translation Options select "Display Both".
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>Textractor/NextHooker
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For an even better translation add names in chiitrans lite, this is because sometimes you will get a literal translation of the word instead of it being recognized as a name. you can highlight the Japanese text on the TL window and right click > add name. If you have the japanese text but don't know what the name in English is supposed to be you can use http://www.edrdg.org/cgi-bin/wwwjdic/wwwjdic and choose "Japanese Names" for the dictionary.
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Info: <https://github.com/Artikash/Textractor>
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Other Translators I like are Google and Honyaku, they're online so you get a small delay with them but if you don't have Atlas these work. Though Atlas surpasses them both 90% of the time (Though Honyaku ain't too shabby when it comes to phrasing). I use these 2 along Atlas just in case the Atlas translation is difficult to understand.
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Download: <https://github.com/Artikash/Textractor/releases>
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Hopefully you dont run into it, but I personally have problems with chiitrans lite. Sometimes it wont load properly as i keep trying to open and multiple instances of chiitrans' exe will be running but no UI that shows up. If you get this problem just keep trying to open till it finally does, maybe right click > "run as administrator" or "troubleshoot compatibility" help, not sure.
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#####Original Guide by /hgg2d/