I've updated my post on The Best Pizza in Taipei to include Zoca on Linjiang Street (near Anhe Road, north of the biggest nightspot area). Really good stuff! Also, I can walk there. Bonus!
I know I should probably actually rank these, but you can't rank something as ineffable as good pizza. I can try to make some order out of the chaos, though.
All pizza places I list below are in the post linked above.
I would say the two absolute best pizza stops in Taipei are now Faust and Zoca - Zoca's great but rather than unseating Faust, it has made it to the great height of rivaling it. For very different reasons, of course: Faust offers low-oil, super thin crispy crust delight with a big focus on the toppings (like the bleu cheese that sends me into rapturous bliss). They only do pizza and beer and I appreciate the minimalist approach.
Zoca is right up there with Faust, but the actual pizza on offer is quite different - softer, slightly thicker crust, tangy sauce, more oil (but in a good way). The beer on the menu is not as good as Faust's one-label offering, but they have some nice desserts going and homemade limoncello. The pumpkin soup was good but not to die for. We didn't try anything else (I'm afraid to get salad at a pizza place anywhere that is not Amore).
Amore Pizza on Xinhai Road is not a step down, it's just very different. So different that you can't even really judge it by the same criteria. Where Faust and Zoca make good, arguably gourmet, pizza, Amore makes New Jersey pizza. You aren't going to find capers, sundried tomatoes, pesto, grilled zucchini or any of that at Amore. You're going to find the pizza I grew up with (I'm from the tri-state area, close enough), with those glass jars in the swirly pattern and metal tops with parmesan, oregano and dried red chili and metal napkin dispensers. You know the jars I mean. If you're from that part of the country, anyway. Plus they make their Caesar salad dressing from scratch, with real ground anchovy. The one place in Taipei where it's worth it to get a salad with your pie.
Just a slight step down from those dizzying heights, but still very good, are So Free and Fifteen. I still heartily recommend either, but for very different reasons, again: Fifteen is the sort of place where you can get pizza with caviar on it and Belgian beer. So Free is bare-bones thin crust vegetarian pizza with just a few choices, a small space with very little seating and generally healthy drinks.
Still good - as in better than Domino's and not a bad choice if you're looking for some decent slice action are Alley Cat (which I used to love and now merely like) and Maryjane's. Alley Cat, to its credit, seemed to be the driving force that brought good pizza to Taipei. I am fairly sure that the other places opened after it did, or around when it did. It's still good, with excellent tiramisu, but I never quite forgave them for screwing up the check a number of times at their Huashan location and I do find that the toppings you get are a bit skimpy (Zoca, Faust and Fifteen are quite generous with their toppings). Maryjane's is sturdy, decent pizza but I wasn't thrown to the heights of rapture with it: their feta cheese was not nearly pungent enough (I was actually not even sure they'd used real feta on my pizza), the cheese was workmanlike and the crust good but not memorable.
On some weird other level, there's Bollywood Indian Pizza. The thing is, I don't include it in "pizza" because it's not pizza, really. It's more like a flat naan with curry spread on it and some cheese, to approximate pizza but really be curry in a different form. It's good. It's not pizza, but it's good.
I still have to try Pizzeria Oggi in Tianmu. I just rarely make it to Tianmu, is all - not my preferred haunt and a bit inconvenient to get to (for me anyway). We'll see if they stack up.