I use muffling on my floor tom. I swear the head (pinstripe) is somehow defective. I have tuned other pinstripes (usually a warm, fat, slappy sound) before, but mine is very, very ringy, and its not a good ringy, either. It goes straight from the detuned buzzy slap to this ringy crap in an eighth of a turn[of the key]. Its a bad ring in that there is hardly any definition. I will see next time I get new heads. I'm most likely going to go for Aquarian coated 1-ply. I'm not very happy at all with Remo... Except for the PS3 bass batter, its good.
Everything else is practically free from muffling. Currently I'm employing a 4-piece, and the high tom has a little bit on the reso head, I will most likely take that off. I'm definantly starting to enjoy the ring of the drums (when I heard Joe Morello, it all changed), especially the snare with the wires disabled, I'm a sucker for that ring. As opposed to when I started, I had tape all around the heads. Ughhh...
I think more experienced players tend to have better equipment and therefore don't need to battle with crap sounds as much.
truth in that. You can get a bad kit to sound good, but its harder.