What can be bought for a civic, down to the smallest detail(without changing the engine)that will make the car run better and faster? I'm talking everything, even if we are talking minimal change in hp/speed.

I'll list them in the order they should be done-
Cold air intake
Short throw shifter
Header/High flow cat/good cat-back exhaust atleast 2.25'', preferably 2.5''
Upgrade ignition-Wires, coil, etc.
Chipped ECU
Better clutch and light weight flywheel
Cam gears
Underdrive pulleys and crank pulley
Upgrade fuel system-injectors, fuel pump, etc
Intake manifold-also bigger throttle body
Cam swap
Limited slip differential
Nitrous Oxide:iceslolan

This is of course if you want to stay all-motor. Forced induction is a completely different scenerio. Also I only listed mods for the engine, I don't do outside that so for suspension upgrades some else should chime in here.

i'll take over for the handling then.
Lowering of somesort springs coilovers
Shocks struts
tie bars
strut bars
sway bars
bushing kit
wider wheels (light wieight)
better tires
lightweight lugs (for looks really)
brakes