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)
-Stuck in a Pose

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. mblock129:
-All bugfixes should work, including the little animation fixes.
-Using Edgar Revealed is not a good idea.

9. Remove the header.

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

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

12. 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, provided you saved these patches for last.
-Rule of thumb: if there's a patch listed in the readme as 'fix patch for a non-headered SNES ROM with _______'s "_______" patch applied' and you've used the listed patch, use it instead of the regular one.  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.  This is the only case of an order needed for this part.
-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.

13. If you wish, Minimap Enhancement or the Music Player should probably go here.  Also some smaller tweaks like the SwdTech gauge speedup, 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.
-Zozo Sign Petty Fix was not meant for the uncensored ones, and therefore it will not look very good.
-Brushless Sketch is known to conflict with other patches.
-As a general rule, any and all fixes about dialogue and other text (description fixes, missing stuff due to bugs, etc.) have already been dealt with by TWUE and then some.  They will overwrite these changes and cause problems.  This includes patches that introduce new text.

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, though I have noted that it works).  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.  It works, but the dash can't be reassigned.
-The restoration of SwdTech Renaming screws with the new Bushido names but it seems to work otherwise.  May end up in the next update.