I'd be interested in this too. One common problem is accidentally doing a tiny face extrude without realizing it: it ends up duplicating all selected faces on top of each other, which isn't always obvious until later and it can be a real headache to clean up.
Merging vertices doesn't fix it--it actually makes it worse. The overlapping faces are still there, they're just sharing vertices.
I could write a script to fix it, but it's not a common enough problem for me to spend that much time on (especially after disabling shift-extrude), but if there's a nice quick way of dealing with this it would be nice to know.
Also, turn off shift-extrude in the move tool's tool settings. It's really awful. This is the main source of that particular problem. If you happen to hold shift for a split second while you're trying to manipulate something, it silently extrudes instead, and if it's a small manipulation it's not always visible. It's a useful feature when you're extruding a lot, but it absolutely should not be enabled by default. Shift-clone for objects shouldn't be either, it's way too easy to accidentally clone a bunch of rig controllers.
