I solved my potting problems this year by getting plastic beer cups from the dollar store and punching the holes by hand. They are taller than the classic 3 or 4" pot, so lots of room for deep roots, and they don't take up as much space in the tray, so I can cram more plants under the lights.
The cups are very inexpensive, and punching the holes (while watching TV) was nearly as therapeutic as the transplanting itself.
I used the 16 oz cups for tomatoes, and a 9 oz cup for the peppers... 30 for $1.