I bought Rayman 2 on GOG a few years ago, and it had a hard time recognizing controllers. I even tried launching it through Steam, which usually fixes all controller problems, but it still didn't work. The Dreamcast version still looks good enough, and your controller will definitely work.
Due to licensing issues, Crazy Taxi 2 has a different soundtrack on the PC from the original Dreamcast version. The Dreamcast version is the one with The Offspring.
Sonic 3 has also had music licensing issues, so the version included in Sonic Origins has a different soundtrack. Sonic Origins was also buggy at launch, but I hear that's fixed now. Sonic Origins also adds a bunch of new features though, so this one may be a tossup.
Question for y'all: did anyone buy the recent PC port of Metal Gear Solid 2? It seems to have both a lot of praise and a lot of complaints.