Sally does look like something in the same general area as text alignment, but I'm not the one to tell how useful it could be... that stuff goes right over my head. My aligner has hunalign do the heavy lifting, I just built a frontend for it with pre- and postprocessing and a bunch of other user-friendly features.

Maybe (or maybe not) you'd be better off having a gui/web interface instead of drag'n'drop to console. Using a console in the first place assumes a certain level of user knowledge, and you might just be better off to get them to specify path instead of introducing the drag'n'drop to console thing into it.

Well, a gui would be nicer and less scary for the users, but it would also be a hell of a lot of work. I'm considering making a gui with tk or something similar for this later on. BTW this started as a windows batch script, which I rewrote in perl to make it cross-platform and expand the functionality. I'm definitely not going back to a single-platform solution unless it's for Windows and it allows me to easily write a more powerful program with a nice gui... probably not even then.
Getting the user to specify a path... that's what I wanted to get away from. That requires the user to have quite a bit of computer knowledge and even then it's a royal pain to do. Most savvy people would end up moving their files to where the aligner is, and most unsavvy people would end up not being able to use the thing at all. IMO drag & drop is the best solution considering that a file browsing gui is out of the question for now.