Nyambe: In addition to being a weird African-inspired, Dreamlandsian d20 setting, it also showed how much you can change the D&D milieu with a couple of rules variants, some feats, and a few specialized classes. Suddenly, D&D is a game about lightly armed and armored wrestler-warriors who practice rituals to honor their ancestors and fight weird sorcerers.
Love and War: First of all, this is one of a proud few d20 products that can be called researched. It's a fun, light read that delivers a big load of historical, romantic, and mythological information about chivarly. But that alone would not get you into the list of the exalted few. On top of that layer, it shows how to deftly combine those tropes with the conventions of a traditional or variant D&D world, and includes some really slick game mechanics that drive a playstyle well-suited to a certain style of campaign.
Occult Lore: Any one of these variant magic systems outlcasses many entire magic supplements. This is my role model in terms of what kind of content a 3pp sourcebook should deliver.
Star Wars Revised Core Rulebook: Why, oh why, did I sell off my collection? Saga was fun, but just didn't work as well. The RCR started off merely good, but it was the Hero's Guide that moved the system into classic territory.
Dawning Star: Operation Quick Launch: I'm biased, but this was a beautiful book that delivered a lot of game. This is probably the only substantial science-fiction campaign published for the d20 Future family. This product hinted at how much the d20 Modern line was capable of... but alas, that lineage lost its development momentum at WotC and became frozen in time. WotC should probably cut Blue Devil Games a check for how many d20 Modern sourcebooks were sold so people could play this; they certainly weren't lining up around the block for Urban Arcana.
AEG's Magic: Eventually, this book would be almost completely obsolesced by other developments, and with 3.5 it became largely redundant. But this book did it first and best: minor variations on arcane spellcasting, totem magic, new feats, weird prestige classes, and so forth.
AEG's Mercenaries: Despite the title, this book was about half mercenaries, and about half a crunch resource for martial characters. Again, eventually this book would be obsolesced, but this was basically the PHBII before there was a PHBII.
Mutants and Masterminds: Looks like a third generation winning streak to me.
Pathfinde: Nuff said.
Fantasy Craft: A quirky and unique, and therefore worthwhile, variation on the old fantasy saws. Customizable, smart, and dramatic.
Adventure! d20: Preserved the wonderful backstory and seamlessly ported tropes from the old system into d20. Shockingly good, especially compared to the fiasco that was Aberrant d20. One of the best pulp games out there... the only complaint I can voice is that the original Storytelling version was better.

An exemplar of a good, holistic conversion that meshes well with both d20 conventions and the source material.
Testament: I had no idea Sunday school could look this much fun. I would totally play this.
Tome of Horrors: The monster book that completes my soul. Everything WotC considered too quirky, retro, objectionable, or redundant, but that was loved by some geek, somewhere. And very thoughtfully OGC'd for the good of mankind.