V1.0 is great for speedruns and is almost always used for them, but it has bad lag at certain times and is low-resolution. V1.1 and V1.2 only removed glitches that are helpful for speedruns, Islamic references that I don't care about, red blood that I also don't care for, and grammatical mistakes which are fine and dandy but don't make up for the glitches.
The both Gamcube versions increased the resolution, lowered lag but still has the lack of glitches problem, and the Gamecube controller just wasn't meant for the game, in my opinion. I do like how it introduced the Masterquest version.
The 3Ds version has amazing visuals but don't bring enough new content to be worth the purchase, in my opinion.
In conclusion: A tie between V1.0 and Gamecube Masterquest.