I would like to know if there is good practices, good tools to move a bunch of windows makefile projects to some msbuid (VS 2010) format? If you think that' not a good idea to make it using a tool, maybe you do know something like a dependency analyser to make a checklist?
Having recently converted a legacy "make" based build to MSBuild, I'd have to say that there is no real easy way. Granted, the legacy build I was working on was actually calling msbuild to build .sln (I believe that the build engineer that put the other process in place was Old-Skool, and was using the toolset that best suited him, rather than .Net).
However, what I noticed was that the make (specifically nmake.exe/build.exe) tools were directory based - subdirs were "built" before parent dirs. Whereas that is not the case for msbuild - it's solution and project based.
Get your code into Visual Studio projects, living in a "flat" directory structure (having all projects as children of a single "Source" folder will really make your life easier in the long run - don't have projects that live several dirs "down the tree"
Use multiple solutions to break the build into "tiers" - order the build of the slns into a helper .bat file - this will help you in the long term to convert to TeamBuild
(my answer started to get out of control - your question reminds me of that joke with the American visiting Ireland who gets lost, and he asks a local "how do you get to Kilarney?", and the local replies "well, I wouldn't start from here".. Can you give a bit more detail about what you are actually buiding? Is it .Net code? I'm sure there is countless advice I and others could give you, but don't know what you are working with)