I actually care about handle length and feel more than blade length. Balisongs may be the one knife type that starts with the handle design first, and then the blade. Keep in mind I am a total noob though - I may be wrong.
Around 4" for the blade seems to be the most popular and the most commonly available. Personally, I like that length the best for flipping, but for carry, I like smaller balis (3" to 3 1/2" blade) better.
The only thing i dont like about a 3" blade is you dont have much handle to back it up. If i were to carry a bali with a 3" blade id much rather have handles from a 4" bladed knife. Hell, at that rate ill just take a 42 and shave a little off the top if you know what I mean. May look slightly odd, but i cant get used to the small handles of things like a morpho. I have a korth panther and that seems a little too small.