TFS Version Control will automatically detect a file's encoding based upon the following.
The only exception to the foregoing is PDF files. Those are always detected as binary because they are so common and can be all text in the first 1 kilobyte with binary streams later in the file. The detection is based on the signature, "%PDF-", that always appears at the start of a PDF file.
So, if you take a file that is in the euc-jp encoding and add it to source control on a US English Windows system, it will be added as Windows-1252 unless you specify a different encoding with the /type parameter on the add command (e.g., "tf add /type:euc-jp file.txt"). If the file is already in source control, use the edit command's /type option to change the encoding.
Within Visual Studio 2005, you can change a committed file's encoding by navigating to it using Source Control Explorer (View -> Other Windows -> Source Control Explorer), right-clicking on the file, and choosing Properties. On the General tab, click on the Set Encoding button and choose the encoding or click on the Detect button and have Version Control detect the encoding using the process described above.
Because changing the encoding requires pending a change on the file, you must have the file in your workspace. Files and folders in Source Control Explorer that are in grey text (rather than black text) are either cloaked or not mapped in your workspace or the workspace does not "have" the file (the server keeps track of what files are in your workspace).
Unfortunately, TFS does not support changing the encoding of a pending add. If you need to do that, you will have to undo the pending add, and then re-add the file using the command line and specify the /type option.