Okay, don't leave taxes on low, with the same governor in charge, for more than four turns in a row. Regularly move your governors & generals. Leaving them idle (with 100% movement points at end turn) gives chances of bad traits (I've had generals get the Lazy trait while besieging a city). I try to make it a habit to rotate all my governors every fifth turn. And if I am looking at a particularly city during the turn, I will move the governor in and out of it. Or try to do things that get the anti-trait to the negative trait, eg the anti-traits to Corrupt are Upright and Loyal, using characters with those traits makes it more difficult to get the bad traits (look over Salisian's trait guide:
http://www.gamefaqs.com/pc/931592-me...war/faqs/50116 )
Eventually you may have a lot of generals and governors, however, and then it becomes a pain (if I end up with too many, I start killing off the less important (i.e. those with too many bad traits or those that are not actually part of the bloodline), and you just gotta live with it, and focus on a few major ones.
edit:
There also, for me, always seems to come a point in a campaign where a whole generation comes of age with the Insane trait, while I find it amusing to play with a character like that, when it happens to a whole lot, then it is time to open the cheat-console...