What I normally do, with drums anyway, is run the gates on the way in. I usually set the release so that it still rings out a little longer then it normally would in the final mix. Then I will normally stick a plugin gate on it with a very light threshold and release on it just to tighten it up a little bit and get rid of as much noise as possible. Then I take it and clean up anything that is missed by the gate with editing. This method has always worked great for me.
The downside is you have to have a lot of analog gates. Not a problem for me .. but for some it might be.
-- Ben