Questions #1 through #4 on the Joel Test in my opinion are all about the development tools being used and the support system in place for developers:
Check out these articles on Continuous Integration using MSBuild, CruiseControl.NET, FxCop, NUnit, NCover and Subversion...
From the software development trenches
I'm currently using SVN but I've generally had a lot or problem with checkouts to a network drive on a dev server. There tend to be locking issues that require a lot of fishing around to fix. It may be that using the WebDav access method, would ease some of these problems, but I haven't experimented yet.
Any of Bugzilla, Trac or Fogbugz will help you with your bug tracking, and each offer an export feature, so you can always change your mind later on. Also, if you can get your team to fully buy in, time management software can also be handy for post-mortems, etc (if everyone is motivated to fully participate.
My preferred stack:
1) Subversion. I'm intrigued about distributed source control but haven't had chance to try any in anger yet. For a centralized solution svn is rock solid.
2) Ant. Maven is a joy to use when it's working but as an old ant hacker I find maven to be hard to follow once things go wrong.
3) Hudson. Not been mentioned so far but definitely worth investigating. Incredibly usable and actively maintained tool. PreviousLy we paid for Anthill Pro which seemed flakey and was painful to fix each time it screwed up.
4) We pay for jira. Not cheap but much more usable than the open source options we looked at and very flexible too.
My engineering stack:
No doubt these choices are influenced by my development stack, which most often includes Ruby, Rails, SQLite, Firefox, and OSX.
I don't think you really need obfuscation on .Net any more (see another response)
I wouldn't consider Vault, SVN is really the market leader at the moment (and free). Git is looking pretty promising but currently is command line only with a steep learning curve.
MSBuild beats NAnt for .Net 2 or 3.5
CC.Net is excellent.