I'm doing a hybrid model: day rate + a "per image" fee. This keeps the shot list reasonable, and also allows me to do really small jobs, with maybe only 2 or 3 photos, without losing money.
Like many of the other architectural photographers here, I'm granting very broad licensing to my architect/design/build clients. Perpetuity, broadcast & display, web, print collateral, local advertising. I exclude National Print, editorial, and of course third-party usage, where I make a lot of money. I do lots of secondary licenses. When you're shooting for someone's portfolio, it's difficult to impose a time limit. I wouldn't accept it if I were on the other side.
Straight-ahead advertising work, on the other hand, has more of a tradition of more controlled rights-management, and I guess I'd be happy enough to play by those rules, if I were in that game.