This bugs me. Why not just use a piece of tape? Nevertheless, I was told by one of the volunteers at Happy Dragon Thrift that hairspray will remove permanent marker from glassware.
It worked! It took a few applications and allowing some of them to just sit for a few seconds in-between scrubbing. But the whole process was only a minute or two. Phew! All that glassware I thought was ruined still has a chance!