Keep in mind; Tunecore gives you ALL profits made from iTunes.
CDBaby take's an addition 9% after iTunes takes their cut.
For an example, let's say you make an iTunes sale for 99 cents.
iTunes takes 30% of that. So now we're down to about 70 cents.
Tunecore will give you the 70 cents.
CDBaby will take 9% of that; so you get about 63 cents.
For me, it's a better deal with Tunecore because that 7 cents adds up as I make sales; also easily cover the 50 dollars I pay every year. I could definitely see CDBaby working better for someone though. Just gotta do the math and try to estimate how many sales you're going to get.
Also I've heard CDBaby makes the process a little harder to get online. Maybe I'm wrong, but that's what I picked up from reading about it..and Tunecore gives you a UPC code for free..from what I read, CDBaby makes you pay extra for that.
They both are probably the 2 best choices out there. Just gotta pick the one that works for you personally.