if all things were equal, im not too sure which wheelsize would be my favorite. However, 700c has entirely dominated the road-riding world for a few decades now, and as such, it's my favorite b/c i know the size/geo i like in 700c bikes, and i can get a zillion different sizes/tread patterns/styles of tires. That being said, this thread has inspired me to try a 650a conversion on my old fuji, instead of a 650b...
having multiple bikes is awesome. if you ever do pick a favorite, it's good to have slightly more beaterish ones for high-risk activities, such as pub-crawls and commuting.
=D
-rob