I don't know what we do differently, but the longest single fight I've been in once a system is known lasted 2 hours and this was 3.5e(18th level home brew adventure). Champions, 2e/1e/basic D&D all much faster for us. Now I've had extended encounters go over 2 hours, but running battles where they get into what could of been like 5 fights i don't think really count.
The fight in 4e with the kobolds took longer, but system mastery is fairly low now so that is to be expected.
Usually for us fights are over quickly like 30 minutes or so. I think the slowest thing for me was mis-matched saves in groups of enemies, I've since made anything that the group fights in large numbers have the same reflex save, so I can just roll a crap load of 20s and know anything above a 14 is a save. I have 5 color coded 20s each 1 representing monster 1-5, then 6-10 etc. I quickly can blow through a list like this.
Outside of that maybe I just game with machines. when the fighter is up, he is like I hit a AC 35, 38, 29, 23 for 28, 35, 20 and 24. Total turn time like 30 seconds.