Auto/manual conversion checklist:
Manual tranny
Flywheel and bolts
Clutch kit (and pressure plate bolts)
Driver's side mount for manual
Shifter assembly
Shifter cables
Clutch pedal assembly
Brake pedal (or grind down your stock one)
Clutch master cylinder
Clutch slave cylinder (if not included with tranny)
Clutch lines
Manual ECU or wire in resistor box for the auto ECU (OBDII, '96 and newer only)
I just wanted to put this down so that I don't have to retype it every time someone asks me how to do it

Feel free to add thoughts and comments.
-Doc