Patching Order:
1. TWUE with Bugfixes (Opera optional.)
2. Add a header.

3. First to get these out of the way:
-Vanish/Doom Fix
-Psycho Cyan Fix
-Rage Patch (optional, but it adds the other unobtainable rages to the list)

4. Assassin17/MasterZED:
All bugfixes seem to check out except:
-What's already in the patch (not listed in TWU's readme but present: Reflect barrier shown on bodyguards fix)
-Magic overflow, present in a later patch.
-Multiple options used (Though there shouldn't be any difference in results, it's your choice which one to use.  These are merely suggestions): Jump Megafix A, Simple Throw Down (Part of) the Gauntlet, Equipment based Miscolored command names.

5. Novalia Spirit:
-All Bugfixes except Remote Control are useful, this is included in a later patch that fixes more things.
-Cursor-focused patches will cause problems within the attack menu.
-Sorting Fix is unneeded.
-Vanishing Magicite and Naming Shadow run into already existing text fixes.

6. Dijibriel:
-Rushing Celes Fix
-Wild Cat Fix

7. Imzogelmo:
-Carve Stone
-M-Tek Vehicle in Cyan's Soul event
-Mine Cart Fix isn't needed; it's already installed on TWUE
-Vector's Cure-Castin' Kid no longer heals the dead
-Gogo and the Cursed Shield.

8. Remove the header.

9. Next add:
-Bridge Correction
-Wrong Way, Idiot!

10. Lenophis:
-Can't Lose For Winning
-Fancy Walking
-Anchor's Aweigh!

11. Leet Sketcher (Note: These are in no particular order unless otherwise mentioned. Remember to check the readme included with each patch for which ones to use on your setup and keep in mind what you've already applied, there's a reason why these are listed so late!)
-Just about everything works in the bugfix section of things.
-Rule of thumb: if there's a patch version that lists that it's for another patch, used if you've used the listed patch before.  Stuff will break if you don't.
-Dead Hare should be applied early.  There is at least one patch with a compatibility version for it.
-Beware of Bye Bye Breath if you plan on doing any editing later.
-Imp's Retort is more or less the "second half" of Psycho Cyan.  You should probably be applying this if you used that.
-If you are using Magitek Madness, just don't apply Side Saddle at all.  SS is contained in this one.
-Self Sneeze contains Remote Control, so you won't ever need that fix.
-Ultimate Damage contains overflow fixes, so you won't need to apply any other overflow patches.  Just use this instead.
-It may be smarter to go with Soul Saved version A given what we're doing with a whole bunch of patches.

12. If you wish, Minimap Enhancement or Music Player should probably go here.  Also some smaller tweaks like King's Robes and Open Eyes Terra would go here, if you feel it is warranted.

Do NOT use:
-Multi-Steal Fix will screw up some names.
-Brushless Sketch is known to conflict with other patches.
-As a general rule, any and all fixes about dialogue and other text (description fixes etc.) have already been dealt with by TWUE and then some.  They will overwrite these changes and cause problems.

Patches that are kind of iffy, and either require additional work or great care when applying:
-Holy Randomness, Batman will overwrite some data found in the original patch.  Using it is not advised.
-The Multi-Font Selection patch would only work with a custom build of it; it tends to conflict in used space (as well as the music player).  It does however, work with the fixed up original font of TWUE.
-The restoration of the button config doesn't jive very well with TWUE due to the B-Button Dash.
-The restoration of SwdTech Renaming screws with the new Bushido names.  May end up in the next update.