I am also a massive fan of Lyx.

I'm only an undergrad physics major, but I'm in 2 classes where I have to submit moderately high level reports, and I'm working on a thesis. And I've only ever had to use one special format, which also happened to be the default format.

So far, I've found documentation to be eh, but I haven't had too many problems where that was an issue yet. The biggest problem is that my knowledge of LaTeX is sorely lacking because I've been using Lyx for everything!