Pop-Up books are the category of children's books most easily damaged-as well as the folds of a pop-up being bent out of shape or ripped, there's the tags which become folded or no longer work.
For quality pop-up books go for date, the same as any book. The pop-up seems to date to Victorian times, so if you see a Regency or Georgian pop-up book be wary!
For modern pop-up book the name Jan Pienkowski may be useful-she created such pop-ups as Haunted House and Robot. It is worth looking for any children's illustrator like Richard Scarry, Dr Seuss and Brian Froud.
Such names as Peter Pan and Alice in Wonderland may be valuable depending on condition. A lot of books going for good money seem to revolve around fairy tale or myth. If you have a pop-up linked to a film or stage musical (like Star Wars) again that is good news.
Even a fairly new character like Pingu can create a collectable pop-up book.
A lot of pop-up books are factual and these are collectable as well-though of course the majority are for children.
What you have to do is research the market, as I've done in writing this piece.