I just wanted to add that I realized that 90% of this functionality already exists in DeckBox. When you go into a specific card in your collection, you can add flags like "Altered", "Misprint", etc. So I would imagine that extending that to allow for a fixed number of user-defined flags would not be a big deal at all (it probably wouldn't even have to change the DB schema).
I'd even be OK if we couldn't name those flags ourselves to start with! Just UserFlag1, UserFlag2,... UserFlag16. Seriously, that would solve 99% of the problem.
In the meanwhile, I've started marking the cards I keep in albums (as opposed in boxes) as "Missprint". That way at least I can find them quickly. I might start taking over some of the other flags to indicate if they're in a cube.