Alright, I can finally get around to answering this.
Things like patch conflicts
There's no possible way I could know what patches conflict with other patches without manually testing everything out there and the kitchen sink.
patch redundancies
See above.
patch requirements (headered/unheadered, release, region, other required patches)
Fortunately, at least for FF6, just about every author I know makes sure to note what is required in those strange text files called readmes. As for the other games, it's up to those that submit. Yell at them.

tool conflicts, tool redundancies, similar patches
See first point.
and possibly a modified download form that lets you put checkmarks next to the patches you want to download, and then you can click a download button at the bottom to get all the ones you want, all at once.
I'm not really sure I like this.
And I can't tell if some patches are just minor tweaks to a single game mechanic, or if they are full-blown modifications to almost everything. Maybe call the former "hacks", and the latter "mods". Or come up with some name to differentiate between the two.
At least for FF6, anything I release as a fix is clearly labeled "fix," and a tweak to gameplay is "tweak." I haven't done so with my FF1 or FF2 patches because there isn't much need for those.

I don't know if any of these things can be done automatically by some kind of script that compares the patches (at least for the patch conflicts part), or if you just have to ask the person who made the patches.
I would need to rework the "database." By database, I mean "one text file that holds everything." It's pretty ghetto.
Some of the patches have ambiguous descriptions.
http://slickproductions.org/ff6patch.php?id=Tweak%20-%20Fanaticism
Both the MagiTek armor events and the Fanatic's Tower area make use of a block of code designed to limit what commands your party can use, and to replace the "Fight" and "Rage" commands with either MagiTek or Magic where appropriate.
So does this patch remove those chunks of code? Does it document it, and give you some options to do various things with it?
I generally copy a portion of "what the patch/bug does" in the readme to that little "about" field for the patch page. In this case, you'd have to ask Ronnen I guess.

I think you need a way to comment on uploaded patches, so users can clarify things like this. Some kind of half-assed wiki would work: something that let's registered users of Slick Productions or Mrognar's Den edit make a comment and then edit their comments, as well as those of previous users.
I've been thinking about a wiki for a while now, but for an entirely different reason. I've floated this to Nightcrawler over at RHDN and he told me it probably wouldn't be rejected, but that I should ask the guy running the wiki first to be sure. He's vanished.

I suppose a wiki here wouldn't hurt, but I think it would be hell to set up/maintain/prevent idiocy.