I voted GBC because, well, someone has to support it. I liked this version because it felt more like a port than the GBA version did. I thought the GBA version added too many unnecessary extras, like the extra dialogue at the beginning of the game and after the boss fights. The only major difference seems to be the addition of two bonus games, Funky Fishing and Crosshair Cranky, which are both great, and a couple of missing warp barrels (which I don't use anyway). The SNES version is still one of the greatest games ever made, but the GBC version has the advantage of being portable. Most of the songs in the original game were cut shorter and lower in quality, but what can you expect from a GBC game?
The only major downsides to this port besides the cut in quality are that the way the characters move takes some getting used to (it's a bit faster), there is occasionally some slow down when too many things are on the screen at once, and this version has different (but similar) music for Gangplank Galleon.
I didn't vote for the GBA version because it felt more like a remake with all of the changes. Many of the sound effects (such as an enemy dying) and graphics were changed, including the backgrounds (which were made lighter), the colors of enemies (changed to stand out from the background), and some of the sprites. The GBC version kept all of these the same, for the most part, and managed to add four additional languages.
To conclude: DKC GBC FTW
Seriously though, this port seems a bit underrated.