Remathilis - I think the reason we focus on player balance is because that's the one that generally comes up more often. Encounters come and go. Unless the GM is continuously screwing up encounters, they tend to even out over time as the GM becomes more experienced with the system. Hopefully.
But, you are right, this is an area of mechanical balance that we should look at as well.
Anyway, back to presenting more types of balance:
7 (maybe) Flavor Balance
This method of balance is similar to setting balance but tends to be more generic. There is an attempt to balance a given mechanic with a presumed in game reality. A good example is the Paladin in D&D. You get lots of powers, but, you also get this honking big role play challenge of a code. Break your code, and lose your powers.
I find this method to be hit and miss. Done right, it works quite well. You get very strong archetypes that can be controlled by the mechanics. The problem comes though in the generic part of things. Again, look at the paladin. Is there a more problematic class in any version of D&D that it appears in? The whole paladin debate has been going on for years and years and years and will never be solved.
8. Carrot and Stick
Here's a balance method that I like. The designers designate certain behavior that is "right" for the system and reward you for doing that. They also designate certain behavior that is not right for the system and smack you with a stick for doing that. Examples of this can include experience bonuses for performing certain actions based on class in 2e D&D.
Like I said, I like this one a lot. Take our Batman example from the Genre Balance post upthread. In Genre balance, the game assumes that you don't pitch the Joker off a roof because that's against genre convention. In Carrot and Stick, you actually add in mechanics that reward players for not pitching the Joker off the roof.
Maybe (and this is off the top of my head) you have a Hero/Villain track. At the high end, you're a big time Hero and people will go out of their way to help you, other heroes will be nice to you, you're the greatest thing since sliced bread. Stuffing the Joker back in Arkham earns you Hero points. OTOH, pitching him off slides you down the scale into Villain territory and you take social penalties, possibly to the point where other heroes begin actively hunting you.
Now, that's what I came up with off the top of my head and I'm sure there are others who could do better. But, I think you get the general idea.