Well, I could do it for about $250. But, that's just cause I know people with the parts. If you were to get the parts from Honda or something like that then you could expect it to cost $2,000+.

You'll need the full pedals, clutch assembly, transmission, shift linkage, all the clutch lines and cylinder...I'm sure I'm missing something.

EDIT: found better info

Parts included with a swap:
tranny
shift linkage
shifter
slave cylinder

Parts you'll need from a 92-95 Civic 5 speed or 94+ Integra 5 speed
clutch pedal assembly
brake pedal assembly
clutch master cylinder
clutch hydro lines on firewall/passenger side frame rail
dead pedal (if you want one)

Parts from a 92-95 Civic
wires that run from ignition switch to the drivers side firewall main clips running out to the engine including the starter relay switch

Aftermarket parts
Place Racing tranny mount auto to manual

Also I know of a link that tells you exactly how to do it, but I can't seem to find it.