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!
LyX fans: Do you have any comments on the relative merits of LyX and TeXmacs?
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