A lot of good points have been made here, but I haven't read anything about documentation yet. If you go with the .net shop, you're going to be up to your ass in documentation of every tiny little detail. Think about what it's going to be like spending half of your time in meetings and documenting stuff.
Also, I work in a mostly MS shop and every time Linux or open source is mentioned, either they give you a dirty look or don't have any idea what you're talking about. There's no tolerance for anything that steps out of the MS best practices framework which only seems to include MS products and solutions.
I've been stuck in a shitty little cube for 8 years now. Take it from me: go for what's fun and interesting and the money will at least be okay. If you're still in doubt, go rent out Office Space before you make a decision. Good luck!