Simplest would be to move the entire directory, and change any my.ini settings as needed. I see about 5 that all point to the same directory (or subdirectories thereof).
If, on the other hand, you need to split the things between drives, it may get a bit tricky. The obvious split would be between
innodb_data_home_dir and datadir
http://dev.mysql.com/doc/refman/5.0/en/installation-layouts.html
has some discussion.
Whether you have innodb_file_per_table ON may be significant.
Alas symbolic links are not useful in Windows, and their equivalent (Junctions) is a bit tricky to set up. (In *nix, I would simply move whatever I felt like, and leave a symlink behind.)
One could debate whether to make some 'intelligent' split of the files (eg logs here; data there. or data here, indexes there), but that rarely makes much performance difference.