http://www.youtube.com/watch?v=bRBZKre9M_M&feature=player_detailpage#t=10s
A visual example to explain the text one.
Generally speaking the current stagelist was derived by trial and error in attempts to benefit less maneuverable/lower tier characters without giving any advantage to higher tiers (the recent trend of pokemon stadium off in neutrals is evidence of this).
It's pretty easy to see why many stages are banned if you understand the basic things that make a 'fair' stage.
Stages are generally excluded if they
1. Have random stage hazards
2. Have permanent vertical walls or walk-off death (this rule was invented for fox)
3. Have the potential for unpunishable match stalling (Hyrule Temple is an obvious one here)
4. Have level geometry that moves/changes in unpredictable ways.
There are still a lot of stages which could be legal by these rules, but aren't. They are usually left to the TO's discretion (Mute city, Jungle Japes, Corneria, et al.) but generally banned for other reasons based on high level observations of match balance.