I grew up in a non-denominational evangelical church – it meant that we weren’t part of any Protestant denomination, like Lutheran or Presbyterian or anything. Most, I think, are pretty run-of-the-mill; they’re not cults, they just don’t quite mesh with any of the established denominations. They may take a page from many denominations’ playbooks (er, prayerbooks). Some of it may also have to do with how the church came into existence – the church that I grew up in started as a Bible study on a college campus, and grew and grew. Churches that are associated with a particular denomination are usually “planted” by an established church, I believe, either because the parent church has gotten too big, or as a mission/outreach thing.
I sometimes wish there were better ways of categorizing non-denominational churches, because they can really run the gamut on a wide range of subjects/opinions. You never know, walking into one, what you’re going to get. You could get extreme fundies or you could get liberals, or anywhere in between.