In my younger years a roll of tape went a long way to getting my a really nice dead 1970's cardboard box studio sound. There was nothing more satisfying than the thuddy sound of a drum robbed of all of its sonic character and tone.
But, fast forward a few (hundred) weeks, and I actually haven't muffled toms in years with the possible exception of some drum dots on floor toms, and I routinely put a Snareweight M80 on the snare. 
I also find that using a tune bot to really dial the tuning in helps eliminate lots of issues that you would want to dampen, rendering a strong fundamental with a great attack and tone that stays pure during the decay.
The bass drum also gets minimal muffling and this time round it's just a felt strip on each head.
In my current situation, there are no close much and I am quite a distance from anyone else so there is no need to tighten up the toms. As to the kick, I have done all sorts of muffing over the years and like the bass drum to be throaty sounding (not boomy) but fast decay.
A friend recommended Drops but they just didn't do it for me. 
What are your go to methods to dial in your sound beyond tuning?
