Even though people have given you a rundown OP, here's what I usually show as differences in the games.>Dreamcast
Superior Music GC(https://youtu.be/lc0PL_rqgU0
Higher resolution (480p VGA possible, whereas 480i RGB on GC. However the PAL release did not get this and it's stuck at 50hz Scart)
Pinta's Quest (Although, all optional items were added in the GC version)
Easier to emulate, but suffers from problems due to inaccurate emulation.>Gamecube
Additional content (Including a side story not in the original, bounties and discoveries)
Better graphics/models (Although, clipping errors due to using a less accurate Z-Buffer)
Lower encounter rate, along with compensated XP to boot technically making the game easier.
Harder to emulate, but much more accurate. Including an option for 3D via Dolphin.
I'd personally go for the DC version, that superior sound quality is just too good and if you truly love the game, play it again on GC with all its additional content is all the sweeter, it's also the console the game was designed for, plus emulation is easier as well as burning a CD if you're into that.
PAL version got badly fucked over so don't play the DC version unless you want some serious slowdown, although I played and finished the PAL version and it's my favourite game of all time. It's a shame there isn't an HD port or sequel