While it wasn't the reason I got back into collecting, Classics et al are now my raison d'etre. To me, the reasons for the lines' greatness are that with the modern advances in technology, they've delivered not only technically superior toys, but toys that matched the animation I thoroughly co-enjoyed while collecting and playing with the original toys as a child. Therefore, my favorite toys are the ones that either weren't available at that time, either entirely, or just in the greatness that they exist now.
In no particular order:
Unicron (Transformers 2010)
How could you make a movie to advance a line of warring toy characters, and not make a toy of the biggest, baddest, bad guy. The Unicron that TakaraTomy made in 2010 is that Unicron. It's absolutely perfect. Earlier versions need not apply.
Skyfire (Henkei or Classics)
I loved my G1 Jetfire as a child, but what I always really wanted, was a Skyfire toy. Heroic, futuristic, I adored that character and his alt mode. While the Classics/Henkei reincarnation is a blend of both Jetfire and Skyfire, the head mold is so perfect (best ever), that it still completely successfully exudes Skyfire to me, making me one happy camper. I have the slightest preference towards the Henkei flavor, but Hasbro outdid themselves with this one, as their version is virtually equally exceptional.
Wheelie (Universe)
I'm sure this one will be contentious. I loved G1 Wheelie, both in the cartoon, and in the G1 toy, although only so far as the alt mode. Not only did the robot mode not match his fictional representation, it was arguably the shittest robot mode in any Transfomer to date. While TakaraTomy blew it with the colors, the Universe version is excellent.
Bruticus (Universe, Fansproject)
I've said it before. This amalgamation of toys, accessories and add-ons represents the greatest Transformers I have ever seen or owned. The fact that half of it was designed expos facto only adds to the awe. Scale, articulation, armament, this guy is what everyone should have always wanted in a combiner. Kudos to HasTak's initial work and IP, and to Fansproject for their extending vision.
I can't come up with a fifth that I feel represents the caliber of these four. I do have a few honorable mentions though:
Thrust, and all of the other seekers (Henkei)
G1 seekers were tight-ass Partformers. Great alt modes, but no fun, and prone to parts loss. The modern equivalent is great, especially the diversity of the four flavors. Thrust just happens to be my favorite, but they're all great, although a bit boring.
Hound (Henkei)
I got the Universe version first, and I really liked it. Then I got the Henkei version and I was in love; the dark, rich green, the great head mold, it's G.I.Joe-Vamp-esque alt mode, and lastly, that gunmetal colored chrome they used on the front bumper is just pure love. It's the little things. ;)
Every other Henkei, United and Fansproject toy
When i think about it, I absolutely adore these lines and virtually all of the toys within them. As I've just finished putting the final toys on my 1986 Movie Autobots display, I really couldn't be happier as a Transformer collector.