Ah, from seeing the board design you posted earlier, I recon you could potentially use smaller pad sizes along the edged if you're going to have through holes anyway. That should buy you some more real estate. And you could also always shrink thins down even more by using 0402 parts. But that's now nitpicking. 
You could still build a reflow-friendly board by having the smallest, or hardest parts on one side of the board (such as the ATMega, regulator, small 0603 parts, and the crystal) and move the large 1206 caps on the other side. Those are easy to hand solder.
Have you decided what you're going to do as far as production of the quantity that you want?