Well, I don't know about POTJ. I didn't get a whole lot, and most of the ones I got where the crappy ones because they were pegwarmers.
My favorite figure came from POTJ, though. Good ole Snaggletooth. Can't go anywhere without him.
Best line has to be Vintage, I guess. I mean, there were figures I loved from all the lines, even Episode I. Vintage easily surpasses that and POTF2, because it was the one I started with. And yes, I did grow up with POTF2 as well as Vintage, so it doesn't mean I grew up back with the Vintage.
Now, there were good parts to all the lines. Though POTF2 had its bulky beginnings, it did come out with a few good figures. The original C-3PO was fine, Garindan and the first Ponda Baba were good. Umm......I'm sure there were others......anyway.....Episode 1 had your Senator Palpatine, Valorum, and Gasgano. POTJ had your Snaggletooth, IG-88, Boba Shek, and many many others. Vintage started it all, and had as many figures as they could pull out. Shame they only didn't have Aunt Beru, Uncle Owen, Wedge, and Tarkin. Yeah, there were a few others missed, but can you go wrong with figures like Squid Head, Prune Face, and Big Blue Snaggletooth? Then there's Saga. Yes, we're in the age of the twenty Anakins, but we've got a Coleman Trebor and a Wat Tambor coming out. How obscure can you get? We've gotten Ephant Mon, Lott Dod, and a dozen new Jedi. We've got these 3-Packs coming out that have Oppo Rancisis, Even Piell, San Hill, and Poggle the Lesser in them! And with a third TV show coming out, we're getting the Clone Wars at our fingertips. And yes, even Durge looks good to me. Boy, it's a great time to be a Star Wars collector!
So, I guess the answer to your question is that I have no favorites. I just love the thrill of the hunt. Oh, and Vintage. Definitely Vintage.