All of the really good stuff has been mentioned so I'll just echo some suggestions:
Skies of Arcadia - one of my favorite games of all time. A lot of people whined about the encounter rate at the first part of the game but fuck them. Everything about this game seems well crafted. The only downside is that some of the later ship battles drag on a little too long but fuck, what a great game.
Grandia 2 - Not as good as SOA but a damn fine RPG. At the time it had an amazing battle system. The biggest weakness is that the game is too linear: you just go from point A to point B.
Evolution 1 and 2 - Got slammed as boring dungeon crawlers and yeah, they're right. I had a lot of fun with these games. It's basically purified turn based RPG gameplay. If you like turn based battling and then grinding to get more abilities, this is the game for you. Everything else (town, plot, etc.) is secondary at best. Don't bother with Time Stalkers, which is garbage. Evolution Worlds theoretically includes both games but I recall they cut out a lot of content.
Basically everything from Capcom: Marvel vs. Capcom 1 and 2, Power Stone 1 and 2, Mars Matrix, Cannon Spike, Project Justice, Tech Romancer, Street Fighter Alpha 3, Street Fighter III (All three versions although the first two are on the same disc), etc. I even had fun with the Spawn game they made.
Sonic Adventure - I'm sure it has aged since I last played it (2000 or so) but it had a few fun levels. The game has a lot of glitches and some of the shitty friends have some real slogs to get through.
Sonic Adventure 2 - Slightly more refined. Has some shitty friends but less so and the game is more polished. Some of the Knuckles levels are bullshit though.
I also had fun with a number of other B/C level games: Illbleed, Blue Stinger (even though the guy walked around like he had a stick up his ass lol), Death Crimson OX, Toy Commander, Trickstyle, Hydro Thunder, Wacky Races, and even Pen Pen TriIcelon is worth burning an ISO for.
Looking at some of the prices and I'd just burn ISOs. Mars Matrix kicks ass but fuck paying $70 for a copy; it came out brand new for $20.