We've used Papa Murphy's in the past. (DD is pn/tn/egg, DH is walnut and soy-allergic, though his soy tolerance is pretty high, and I'm sfa.)
Generally, though, we rely on local pizzerias rather than chains; I speak with the manager and double check the info any time there are any menu changes and otherwise about every six months or so.
There are two local places (of about seven-- we're in a college town) which are safe for DD and I both (well, okay-- reasonably so... since both have menu items with our allergens in, but they're also pretty careful). There is just one which is okay for all three of us; we aren't sure what's up with the other place, but it has made DH sick about three times, so we think that something in their dough or sauce recipe has changed recently and now includes a lot more soy. They've added a gluten-free line, so that may be part of it. Anyway-- long story short, we have discovered that for us personally, the combination of cluelessness, poorly trained employees, and CYA from corporate leads to most chains being out of our comfort zone.
I've only run into one pizza place (on vacation in Port Townsend WA-- Waterfront Pizza, if anyone is up that way) that was truly free of ALL of our allergens-- it was so nice to eat there. It was also really good pizza.
