Seat the head first. Press firmly on the center of a new or freshly-installed head to pop the collar into place before you start tensioning — otherwise it will keep settling and drifting out of tune as you play.
Tension evenly in a star (cross) pattern. Never tighten lugs in order around the rim — work opposite pairs in a star sequence, giving each lug a quarter to half turn per pass, so tension builds evenly across the head instead of pulling it into a warped, unevenly-pitched cone.
Tune batter and resonant heads as a pair. A common starting point is tuning the resonant (bottom) head slightly higher than the batter (top) head — this brightens the tone and shortens sustain a bit; tuning them to the same pitch maximizes sustain, and resonant lower than batter deepens the tone with a pitch bend.
Tune toms as a descending musical interval down the kit. A pleasing, common approach is a minor or major third between each tom (high tom → mid tom → floor tom), so the kit outlines a small musical phrase rather than random unrelated pitches.