I was thinking about something similar; having a Sort Field like iTunes does, where, despite the actual name of an item, you can type something else that it looks to for sort order. It would have to be a field for the issue in the user's collection, not for the issue in the database, so individual users could customize their own collection.
The 'My Collection' link could have a 'list using sort field' check-box to determine if the sort field is used to order the collection or not. When sorting and using the custom sort field it would use the custom field first, then the actual indicia name. It should still display the name as it is on the indicia, it is just ordering it elsewhere in the listing.
For example, if you typed 'Spider-Man' in the custom sort field for all of your "Spider-Man" titles. When displaying the collection with the custom sort field turned on, it would list your collection something like what I show below. "Southland Tales" and "Strangers in Paradise" just showing as a title before and after "Spider-Man" alphabetically.
Southland Tales (2006)
Amazing Spider-Man, The (1963)
Friendly Neighborhood Spider-Man (2005)
Marvel Knights Spider-Man (2004)
Peter-Parker the Spectacular Spider-Man
Web of Spider-Man (1985)
Web of Spider-Man (2009)
Strangers in Paradise (2004)