Stonington Pizza on route one near the Boro is awesome! The BBQ Chicken Supreme is the best pizza I have ever had hands down. I would stay away from Mystic Pizza, too many tourists, too greasy, expensive and run of the mill.
I personally LOVE the mashed potatoe white pie from BAR in New Haven. Don't knock it until you've tried it. Pepe's in New Haven is also great, but slightly overrated (people come from all over the world... dunno if I would do all THAT, but it is extremely good).
There is a little place in Ansonia called Roma Pizza that is great cheap brick oven. No delivery, but you want to eat this stuff fresh out of the flames.
For greek style, I haven't found anything better than Zois in Seymour. The sauce is great, and is heartily measured onto the thick puffy crust.
+1 on the mashpotato and bacon white pie at bar, with their stout.
in fairfield I'm a fan of tomato basil they have a small but impressive beer selection (4 on tap, always an ipa and none of the usual sams, guiness, mbc's)
Jimy bobo's in stamford (colony) is an experience.
Bar in New Haven is my favorite. Really good pizza (maybe not the best in CT, but the atmosphere and the brewed on site beer makes up for it). In my opinion, I think Sally's is the best pizza I have ever had but I hate waiting 2-3 hours for it!
Another pizza place opened up next to me in Monroe that is excellent- Julian's- Almost as good as any pizza found on wooster st.