I've been drumming since I was 15 (I'm 23 now). It's taken me years to get a good sound out of my drums (I only use a Pearl Export that I bought in the mid-90's for $600), but I've developed a method that yields compliments from the engineers in every studio I've gone to record at. Over time you'll develop an ear for what sounds good, but here is the basic formula that you should follow.
The most important thing to remember about tuning is that you have to tune to the drum, not to the pitch that is desired. Please keep in mind this is a lengthy process and can drive anyone else in the room nuts (including yourself). But it is well worth it, especially for a quality recording. It also helps to increase the volume and clarity of the toms if your using overheads and not micing them direct.
OK, here we go:
As far as the toms and the snare it is pretty much the same. You should start fresh with both heads off the drum. Put the bottom/resonant head on first. Settle it on the edge of the drum, place the rim on, and hand tighten the lugs until they rest firmly on the rim. Then tighten each lug in a star type pattern w/ your tuning key. Keep going around the head in this star pattern (in complete cycles, to ensure that the lugs are equally tight) until the head is tight enough that it doesn't have wrinkles. After it is at this point you need to continue the star pattern, but tighten the lugs by smaller intervals and hit the center of the drum with a stick after each lug to hear it's tone. Keep doing this until you hear the head resonate a solid tone.
Now to fine tune, keep hitting the center of each head with a stick. Go around each lug and tighten and loosen it back and forth. You will hear how each lug affects the overall sound of the drum, so just tune it where it sounds good.
Once you get a good tone from the resonant head on the first drum, move down the line and get all of the drums to their respective tone. If you have 12", 13", and 16" (standard sizes) they should sound roughly like 3rd intervals. If you are confident in your hearing, You can then make minor adjustments to each one to give them closer to a relative pitch, but they don't have to be tuned exactly to a given pitch or be an exact interval. It is more important for the bottom head to resonate clearly with the drum.
Now on to the top head: Make sure you have the drum mounted to the kit/stand so you get an accurate representation of the true tone you'll get from the drum. You do the same as the bottom head, and eventually get the drum to resonate a good solid note. Do this around the kit and you're finished.
The snare ALWAYS sounds best when the snares on the resonant head are not too tight. Get a good sound out of your drum first without them on, and then gradually tighten the snares until they sound good.
The Bass drum is the easiest. To get a good solid attack and deep kick, tighten the playing head using the above method until you read the desired tone. Put on you resonant head and tighten the lugs so that there are no wrinkles. Start tapping the center of the head with your finger. Make slight adjustments to each of the lugs until you start to hear a low note form. Stop right there, and you should be happy with the sound.
After this initial setup they stay good for a long while. From time to time follow the fine tuning step to compensate for weather conditions, getting banged around moving, or just to spruce up your tone.
** Oh yeah, if you notice major dents in the heads when you take them off, they'll never sound good... just replace them.