Use this procedure to determine what needs to be done to correct any problems and to decide which steps to take by way of tuning. You'd be surprised how little it takes to tune out excessive rattle from the snares. The last resort to getting your drum sound is muffling. I only do it when time constraints rule out tuning and experimentation or if the drums just plain sound bad. It also helps if you bring an extra snare to the session.
Floor toms suck.
Because they have at least three legs grounding out the shell, thus affecting resonance. Try to get a musical tuning and tone so that your toms actually sound as if they are on the same kit. Try hitting the kick drum to see if you're getting any sympathetic resonance from the toms. Usually you get this from the floor tom or one of the lower mounted ones. Remember that the toms will likely be miked far closer to the heads than your ears are when listening, so what might seem like a slight ring in your toms when the kick is hit could sound like thunder in the control room, and left this way will render you a muddy sounding drum track.