PenDOS (included with PC DOS 7 and higher (and some 6.x versions, 6.3 I think) could do it if you had a menu that could react to the mouse.
If you could get something like EDIT to respond to the pen, I suppose you could echo a few choices out to a file, edit that file, swipe and delete the one you don't want, then have something read that file back in to something that will boot an OS based on that. All in a batch file of some sort.
Or if you can get your own menu program to respond to the mouse (and then the pen), that would be fairly effective too.
Thought I saw a freeware boot manager that would react to the mouse (does Ranish make a boot mgr?). Might have been OnTrack though...
Guess it depends on how badly you want it...