Yes, the d20 boom produced a lot of books that just plain sucked. (I may have produced some of my own that I'm frankly glad have since disappeared.) But there were plenty of games that managed to shine among all the dross. Here are three of my very favorites.
Mutants & Masterminds 2nd Edition
Green Ronin let master of the supers RPG Steve Kenson mold the d20 rules into a worthy successor to Champions not once but three times. My personal favorite is the second edition, and over the years I managed to get everything they put out for it. M&M lets you create just about any kind of super-powered character you can imagine, and the hero point and power stunt mechanics are essential reading for any designer working in the genre.
Following off their phenomenal Spycraft 2nd Edition, Crafty Games took a stab at the original, creating an ultra-crunchy toolkit game to craft your own fantasy adventures. This one hits all of my buttons for detail and customization, complete with gear upgrades and a foe creation system that lets you create a monster once and scale it to any threat level. Unfortunately, the extreme detail means I am unlikely to ever get this one to the table. I've also long since given up hope that Crafty will ever release the promised magic supplement.
Call of Cthulhu d20
After the success of D&D Third Edition, WotC turned to licensed games like Wheel of Time and Star Wars. They also did the unexpected and licensed the classic Call of Cthulhu RPG for a d20 adaptation. Certainly, the system lends itself to more action than a traditional Lovecraftian game, but for certain pulp-inflected takes on the genre, it works quite well. In many ways, it's a better modern d20 game than d20 Modern, which came out a few years later. The graphic design is better than just about any of its contemporaries. And finally, this game has some of the best GM advice of any RPG I've ever read, horror or not. If you can find this game in a used bin, grab it.