I am currently running a pair of 1020 mah li-ion batteries stacked on the mini-zx project I previously mentioned. I purchased those before discovering the li-poly batteries. I got them off of ebay as a pair of cell phone batteries for $4.20 each plus shipping. I removed them from their plastic case to save weight, removed the overload protection circuit (you may want to leave this on just to be safe but most r/c lithium chargers are designed to charge without this circuit), and then soldered them together to make up the pack.
In my opinion li-poly is the better choice. I just purchased 4 of those to play with in different projects I am working on.
This is the cheapest source I have found for li-poly cells:
Bishop Power Products