Many times, tom toms are the bastard sons of the drum kit.
We as engineers spend a considerable time tuning the kick, baffling it, tuning the snare, getting the right heads for it, but toms are often overlooked.
I think it's important to put some effort into this part of the kit, but one simple thing you can do is tune the toms to the key of the song. A simple place to start would be the root and fifth of the key of the song you're recording. You can of course tune the toms to any note in the scale of the song, but I think tuning the drums to the key of each song is any easy way to unify the drum sound and any tom grooves to the rest of the instruments in the recording.
