Favorite house rule
Hmmm...I've got two, both from Champions, and one was less of a house rule than just an experiment. That was adopting a no initial points limit approach. Instead of building a starting version of the hero and trying to make everything balance out with Disads, we built the hero we wanted to play, chose the Disads that were appropriate, and got on with our lives. The interesting side-effect of this was that we stopped worrying about character advancement, XP, etc. Along the way, we developed some interesting ways of keeping the game engaging, and those turned into my first ever paid RPG work (an article in Digital Hero Magazine). But it wasn't much as house rules go.
The other one is my "SPD = Spotlight" rule for Champions, which has served me well through the years. Given its simulationist roots, it's pretty common to treat a character's Speed score as a concrete simulation of how fast he or she is. But really, it's a measure of spotlight time and all PCs should get the same amount. So, I lock PCs at a SPD of 4 in my supers games, 3 for non-supers. NPCs, I leave alone. They can almost always use the extra phases for defensive actions, and the heroes typically have numbers and plot on their side.
"But what about speedsters?" I hear you ask. Or Bruce Lee level martial artists? I counter by noting that Speedsters in M&M only get a single action and no one complains. Champions is full of ways to attack multiple opponents, cover lots of ground, and go before everyone else without taking seven or eight actions in a twelve-second game turn. Be creative!