For flat cells, go to Hobbyking, just look up the 1S cells and you'll see the bare ones. They're super inexpensive and the quality is pretty good.
For round cells, you'll want to use use the IMR type if they're smaller than 18650. Sometimes you can get away with the ICR 18500s (normally protected), but you need to be aware of your load requirements and the drain limits of the cell.
The smaller IMR cells all come from China for the most part. The AW brand has a decent reputation. There's more brands of Chinese batteries than you can shake a stick at so probably best to stick with one of the more popular ones. For the 18650s, higher quality Japanese cells are available.