Hello. I can relate with what you mean with OS X PPC vs. Intel, when an app is Intel-only, because the download link just says "Mac OS X" and isn't more specific until you scroll down. For OS 9 and earlier, I feel it's less an issue, because the download links on the right will specify if the app is OS X, OS 9 & earlier, or both, before having to scroll down or trying the program out.

And here's the issue: how would we handle apps that are, say, both Mac OS 8.6 and Mac OS X 10.5 Leopard compatible? (Like many Carbon apps, i.e.: The Sims, Diablo II etc..)

In my opinion, this sort of experience that you mentioned can be mitigated, but not entirely avoided, because it's inherent to software libraries as a whole... Even if we separated OS X from the rest, there were times I wanted something for OS 9, but exceptionally it turned out to be OS 8 & earlier only. At other times, the app may even be compatible with the desired OS, but then it is limited to only G3s, or G4s, or G5s, or 68k, or pre-G3 PPC, or specific to a Macintosh model (i.e. a Macintosh II demoscene demo, which I did come across). All sorts of such cases do pop up.

Not because of this, there was a time many, many years ago here during which some few people didn't want OS X software here (and due to the 10-year rule, most of it wasn't old enough to even be here back then), with some arguing that should be on a separate website similar to the Garden. I think differently (pun intended), for the reasons above (else there would be redundancy), and because a lot of software for "Classic" continued on with OS X, and some people may know the Classic counterpart, wish to update it further, and will have it in the same website for their OS X machine (i.e. Toast). Among countless of other such situations.

Still, I understand the sentiment.
But TL;DR:
- It can't be helped. Issue is inherent even without OS X;
- Redundancy is avoided.

For improvements, maybe the Advanced Search function could be expanded to include options like picking the architecture (68k, PPC, Intel) and the OS (1 ~ 9, X)? And/or different filters could perhaps be added to the complete list of the software? Though the latter would be a problem, because each of the pages are updated all the time regarding system compatibility.
In any case, maybe these may serve as food for thought?

I beg to differ. I am strictly 68k, but I stil like to see what happened in the early PPC & Intel days during my searches.
After all, this is supposed to be a historic site first and a download repository second.

Once we split the site of an already small community into yet tinier islands, we'll end up with groups of under a dozen people, just talking to themselves.

An Advanced Search option that breaks down chipset architecture (68k, PPC) or MacOs version (1-9, X) would be helpful if user is looking for a specific piece of software. However, I do have to confess that I downloaded Diablo II thinking I would have to use Classic Mode to play it, but I found that the game works very well in Tiger. So I can see the issue Jatoba described and how redundant and confusing it would be for the user.