I like a lot of the tweaks from Pathfinder Beta (found free at paizo.com).
I like importing healing surges from 4e.
I like a lot of variants from Unearthed Arcana (found free under variant rules at
The Hypertext d20 SRD (v3.5 d20 System Reference Document) :: d20srd.org) particularly spontaneous divine casters and a modified version of recharge magic.
I like a lot of the options from the Trailblazer preview by Bad Axe Games.
Tome of Horrors Revised is a great 3.5 monster book converting tons of the old D&D monsters, great if you want to convert old modules. Tons of other great monster books to choose from.
Spell Compendium is a great spell resource, though you have to watch out for individual spells carefully.
I like Fantastic Science by EN Publishing, it has tech as a third/fourth magic source after arcane/divine/psionics that only works in suppressed magic and sports both a serious point based caster and a warlock style always useable caster class.
I really like the psionics mechanics of psionic focus and soulknife power recharging, so I go with srd/XRP psionics and expansions such as Untapped Potential (et al.) and Hyperconsciousness.
Magic Items: I hear good things about the magic item compendium. I also like Arms and Armor 3.5 and From Stone to Steel, for weapons and armor stuff (both magical and normal).
Campaign Settings: a ton of great options.
Modules: a ton of great options.
Counters: a ton of great options.
Maps: a ton of great options.
Class/Race/Terrain books: ton of great options.