Depending on the Year/Engine, you should pull of the EACV (Electronic Air COntrol Valve) on the back of the Intake, and clean it out with carb cleaner...
Otherwise if that gets backed up, your idle will start to bounce....

And I saw someone said lube the Balljoints, I'd like to mention to do that ONLY if they're not sealed...

O2 sensor maybe wouldn't be too bad of an idea...

Check the valve clearance may be another strange one to try...

Timing belt + waterpump (if the WP blows, you need to take of the timing, so may as well drop the $60, and do it all at once).

I ALWAYS use NGK wires and NGK V-Power plugs in my Hondas. I just use an AutoZone cap and rotor button.

Here's my basic list of things I do to my Civics when I first buy them with unknown history (assuming nothing obviously wrong, like CEL's, etc):

*Plugs / wires / distributor cap / rotor button
*Replace all fluids (coolant, tranny oil, engine oil, etc) and filter(s) and flush coolant system
*Inspect and replace all suspect rubber coolant hoses.
*Replace the thermostat and gasket
*Water pump / timing belt / tensioner / spring
*Inspect and replace oil pan & valve cover gaskets as required
*Re-set the timing
*Replace air filter

I rarely worry about the fuel filter, but maybe I should - it isn't that expensive.

Start out by getting a shop manual, the first chaptor in the book is a list of matince that needs to be done, and the intervels that you should do it.
Check the PCV valve, check the EGR valve, adjust rocker arms/valve clearance, check the battery, flush the brake fluid, chaing the tranny oil, clean the air intake.
air up all your tires, jack up each corner of the car and check wheel bearings, check brakes for wear and draig, check alinment, inspect all of the suspetion bushings, and all of the moving parts in the steering, asjust the play in the rack and pinion.

ahh yes the ol timing belt, DEFFINATELY DO THIS!!! i dunno if that engine is a non interference engine (meanign if the belt snaps are the open valves going to get smashed by the piston?) i know my chevette sisnt so if it snaps ehh...(replaced it 2 years ago so its fine)

Thanks for all the suggestions guys. I'm waiting for weather that's a bit warmer than right now (no garage) to be able to work outside and it looks like there is a lot more that should be done than I initially thought...