Maybe I'm using apm wrong, but I recently found that I had piles of old versions of plugins stored doing nothing in ~/.atom. Deleting them didn't change performance, but did save some space.
...but then I see Hydrogen more or less turn Atom into Light Table and it makes me slightly willing to put up with the madness
! I've been loving some of the other utils people have shared here, too! I don't know how I was living without a clipboard mgmt extension for so long 