https://sukebei.pantsu.cat/ - Nyaa Replacement. When in doubt use moonrunes from VNDB or developer name and find a pack. 18+ only.
https://nyaa.pantsu.cat/ - Same as above, for all-ages titles.
https://sukebei.nyaa.si - Nyaa alternative.
https://nyaa.si - Nyaa alternative, for all-ages titles.
http://animebytes.tv/ - Private tracker, requires invitation or application to get an account. Generally pretty good place to find translated, or even relatively well-known untranslated games, and new English releases tend to be uploaded quickly.
https://gazellegames.net/ - Private general games tracker, but has a decent selection of VNs available. Be sure to enable viewing of adult content in your profile settings.
http://erogedownload.com/ - Fairly comprehensive listing of translated titles, uploads are quick and live links can usually be found, though speed isn't great with a free account and split links can be an annoyance. Use JDownloader to help with this.
http://www.anime-sharing.com/ - Forum with links to a lot of stuff posted. No guarantees of live links or non-bullshit hosts, but a lot of otherwise hard to find untranslated stuff (including a lot of random DLsite H-games) get posted here.
http://www.erojiji.net/index.php?/forum/8-craneanime-visual-novel/ - Old craneanime uploads, new stuff does not seem to be uploaded anymore and the main site is down, but you can find their old stuff here.
http://www.vn-meido.com/k1/ - Old /jp/ sekrit club, you can use it if you want I guess.
Status: Up as of 28/03/2019
http://tss.asenheim.org/ - Provides web-based ports of a few older visual novels and dating sims.
JDownloader: http://jdownloader.org/download/offline - Useful tool for automating downloads of large amount of DDL links. Get the beta version for proper support of the host erogedownload uses. Now with extra adware! Just be very careful to decline or skip the offers as they come up and you should be ok. Read prompts and buttons carefully, they will try to trick you!
VirusTotal: https://www.virustotal.com/en/ - Tool to scan a file up to 128MB with a large variety of antivirus programs. Useful when you're not sure whether a particular download is trustworthy, though as always use common sense.
AutoHotkey: http://www.autohotkey.com/ - Not directly related to downloading VNs, but a very useful program that allows quick and easy remapping of keys on a context-sensitive basis, as well as setting up a wide variety of macros for various situations. Useful if you dislike the default hotkeys for a VN and the game does not allow you to change them. Example script here shows some functionality: http://pastebin.com/k6WyAWuA Get window ahk_class names from the included Window Spy tool. (right click AHK icon and select from context menu, then focus the desired window)
7-Zip: http://www.7-zip.org/ - Free open source program that can extract most commonly used archive types.
WinCDEmu: http://wincdemu.sysprogs.org/download/ - Program for mounting disk images of various formats, necessary to install many of the games you will download.