One important point is to set up your projects in source control such that you can immediately build, deploy and run after checkout.
That means you should also checkin helper infrastructure, such as Makefiles, ant buildfiles etc., and settings for the tools, such as IDE project files.
That should take care of the setup hassle for individual projects.
For the basic machine setup, you could use a standard image. Another option is to use your platform's tools to automate installation. Under Linux, you could create a meta-package that depends on all the packages you need. Under Windows, a similar thing should be possible using MSI or the like.
Edit:
Ideally, instead of checking in helper infrastructure, you check in the information that allows the build to generate the helper infrastructure. This is the approach taken by e.g. the GNU build system (autotools etc.), or by Maven. This is even more elegant, because you can (theoretically) generate infrastructure for any (supported) build environment, thus you are not bound to e.g. one specific IDE, and settings in the helper infrastructure (paths etc.) don't need to duplicate the main project settings.
However, this also a more complex approach, so if you can't get it to work, I believe checking in stuff like IDE files directly is acceptable.