You should label the versions of source files that make up your build. If you're using TeamBuild, it does that for you automatically. It combines the name of your build definition, date, and the build number. So you don't need to do anything.
Your other option is not very conventional and requires a lot of unnecessary work. If I understand it correctly, you would check out your source files during the build process and then check them back in with a version number specified in the check-in comments. This is as Alex mentioned very resource intensive in terms of your build process and also your source control repository. Moreover, how would you get the source files for a particular version if the version information is embedded in the comments? It will be very hard and you would have to sit down and write your own application that uses TFS source control api to download the source files to a workspace by searching for the version number in the check-in comments. This creates unnecessary complexity and headaches.
If you use labels instead, you can do a get by label in VS IDE to download the source files that make up that label. You can even tell TeamBuild to use a label instead of downloading the latest source files during build automation. That way you can build previous versions of your application easily. With labels, you can also apply later changesets to an existing label if there were code changes by simply getting that label and then getting specific changesets and then doing a quick label or creating a brand new label.
Labeling is very powerful, convenient to use, and is a part of TFS. Rather than coming up with your custom solution that requires a lot of effort to make it work and maintain, just try to use what's already available.