Okay so I am hugely frustrated with one aspect of D&D 3.5e, and what appears to be a Universal problem with WoTC-the inability to properly cross reference or index.
I can't tell you how many times I've gone to look something up, only to find no mention of it in the glossary, index or anywhere despite knowing it is in there somewhere. Or worse how many times you're told to refer to another rule entirely with no page or book number! This is maddeningly frustrating! (Especially from a gamer who is used t the cats at Shadowrun, who've always done a good at Indexing, if nothing else.)
But as I write this I wonder how important is this to you? How much importance do you place on functionality? What systems do a good job of organizing their materials? Which don't?
D&D 3.5 Consolidated Lists archive:
http://www.wizards.com/default.asp?x=dnd/arch/lists
I'm a huge fan of indexes for reference books. WotC does better than a lot of games IMO. The best I've seen is probably ICE's Rolemaster and Spacemaster lines. The books themselves can be somewhat haphazardly spread out, but the indexes are tops.
The worst I can think of would be White Wolf. They start by putting a 30-page short story in front of the table of contents, so you have to dig around just to find it. Their indexes are even worse because they categorize everything. For instance, you won't find Coatlicue under C. She's under t for Titan Avatar, subsection T for Terra. That's great if you know exactly what category your target falls under, but completely useless if you just want to find a Griffon (T for Titan -> T for Terra -> L for Lesser Creatures). (I don't have a book handy, so those examples are probably a little off).
Another bad side effect is that you can't just scan the index because the terms aren't grouped by letter. The section headings are, but when you see Heracles you're not in H you're in G for Gods. If you see Dodekatheon you're either in G for Gods or P for Pantheons, not D.
A 100+ page rulebook needs good cross referencing and indexing. WOTC isn't bad at it but they aren't good. I've had games that have no table of contents or index.