My worst experience was in a head-to-head football league last year. When the commish set up the league, he screwed up the settings: you got one point for EVERY return yard! This meant returners were radically more valuable than anyone else.
It was clear that he made a mistake, and I alerted it to him repeatedly before the draft. He didn't change it, so some people drafted with an eye for returners. I didn't, since I assumed it'd be fixed eventually. It was - after the second week of the season. This left those who'd drafted returners angry and made the first two weeks a mess.
And then he disappeared. He had been inactive since he set up the league - I don't even think he attended the draft - and went bye-bye for the rest of the season after week 2. Complete jerk - he was obnoxious and arrogant during his brief return visit - and a terrible commish. That league was a disaster.
I know everyone's down on Yahoo public leagues, but at least they don't suffer from idiot commisioners like this guy!