This is a HUGE TOUGHIE for me...
Alternators has the best OVERALL molds, designs, and collectors appeal in my opinion. But Alternators suffers from too many repaints syndrome and no storyline to go with it.
G1 has the most memories and is closest to my heart, even with the low-to-no posability and the out-dated designs some of them have.
G2 was too bright and garish and plain cheesy in a lot of ways. Now the comics ruled, but the toys...man they were just so "eye catching" to put it nicely.
RID was a nice blend of G1, G2, BW, and BM toys. One of my favorite All-Time TF's comes from that line...RID Scourge (aka Dark Convoy). That toy alone makes RID amazing...not to mention the great Car Bros and various other toys.
Beast Wars didn't start getting good IMO until the Transmetals and Fuzors came along. The first year of BW toys, weren't that good, even though I have a bunch of them. Transmetal Megatron, Optimal Optimus, and Rampage are some of the best toys from that line and all deserve good recognition, IMO.
I only bought two Beast Machines toys...Tankor and Jetstorm. They only two good toys in that line, IMO.
Cybertron has some great stuff. Energon had a few good ones mixed in there...like Energon Galvatron. Armada...well I liked the Mini-Cons and like two molds...the rest was crap...again, IMO.