What color are the folders? Are they a lighter color that printer ink will show on?
I do have a few sets of letter stamps that can be stuck to an acrylic block, and also a few sets of JustRite alphabets that would do what you want, but you are right - the little individual letters are somewhat challenging to work with, especially when I'm assuming that each folder will be stamped with a different name.
The image transfer method that AngelNorth described works really well. Another method I've used that gives a pretty crisp transfer is done with a laser printed copy. You still print in mirror image, then to get the name to transfer, you lay it onto the item you are transferring it to and dab the back with a cotton ball soaked with acetone (or acetone nail polish remover).
The cons of the acetone method are 1) The Fumes!!!! and 2) you'll need to test the colorfastness of the folders - the acetone can fade it.
~~Cheryl, with a "C"