If you find yourself in the situation where you're developing in Windows and using msysgit, and your repo has a conflict, merging can be a painful experience. The best thing you can do is to do it manually. There are plenty of nice tools for merging in windows, but none of them (at this point) seem to work with msysgit. Just read the documentation on merging, and do it by hand. This is explained nicely in the docs:

http://www.kernel.org/pub/software/scm/git/docs/git-merge.html