I have an 03 honda civic ex. It cranks and runs. But when I put it in drive or reverse it acts like it's in neutral. I don't know where to even start on trying to figure it out.

 

Engine runs, but vehicle does not move in any gear:

Low ATF level - use only OEM Honda DW-1 ATF
Shift cable broken or out of adjustment
Shift cable worn
ATF pump worn or binding
Regulator valve stuck or spring worn
ATF strainer clogged - internal clutch debris over time has cause a restriction in ATF flow to properly change gears
Mainshaft worn or damaged
Final gears worn or damaged
Transmission-to engine assembly error
Axle disengaged

Have you done any drain and fills of Honda DW-1 ATF every 30K miles? Do not flush the ATF. If not, the trans could have failed.