I prefer Giana for nostalgic reasons, and I'm not as big a fan of any Mario games that the rest of the world seems to be. I think they're a bit boring. It deserves its status as an innovator (or even pioneer) of the genre, but its severely overrated, just like Sonic. I mean, they are good games, but I still feel completely cold when I play them.
I'm pretty sure it depends on what games you grew up with, though. I was well aware of Sonic and Mario, and I prayed for Sonic in particular to come to the Amiga, but now that I get to play them, they don't give me anything at all. I still prefer Supefrog above all others. It's got a certain charm that I can't resist.