Well, I always went with Cyndaquil most of the time ^_^ It's just adorable, I really like Typhlosion because he looks amazing and I like Fire Pokemon a lot in general ;)
But, there were times I chose Totodile too, so it's a close call :) (not as often as Cyndaquil though).
But hey, if I REALLY had a hard time choosing, I just "took" all three starters using the cloning glitch xD So in the end, I would have obtained all three of them and trained them in my team :3