Ok here goes. I'm also including pre-TFs as well as some of those weren't made into G1
Pre-TFs: MC-18 Magneman. The gimmick is inspired while it manages to also shrink down the basic design of Soundwave at the same time. Simply brilliant.
Gen1: All the Turbomasters and Predators (I'm naming 12 here- deal with it). They managed to take the G1 toyline in Hasbro distribution markets and breathe enough life into it to give us G2. The line has intelligent gimmicks and great designs with classic styling.
If it wasn't for this line coming out, I probably would have walked away from Transformers at age 12.
Alternator/Binaltech/Kissplay/Alternity - Tracks and Hound. Both designs managed to stay true to the G1 originals but
Gen2: Dreadwing, Tank Megatron and Laser Rod Prime. All 3 are simply brilliant in their designs.
Beast Wars - Polar Claw and Optimal Optimus.
Robots in Disguise/Car Robots - Mach Alert, Speedbreaker, Brave Max, Omega Prime, JRX, Build King. So many brilliant toys in the line. Another line where I have to list more than a select few.
Armada/Micron Legend - Overload
Energon/Superlink - Optimus Prime, Wing Saber and Omega Supreme - the most awesome Sentai style toy to ever grace a Transformers line.
Cybertron/Galaxy Force - Cybertron Defense Team. They're not a homage of any kind and manage to hold their own as original characters and toys brilliantly.
Animated - N/A (never really grabbed me- Ultra Magnus if I had to pick one)
Classic-verse/Henkei/Generations/Universe2/etc - Prowl, Bumblebee, Optimus Prime, Megatron, Seekers, Jetfire, Wheeljack. Brilliant Homages all round.
Movie-verse - Bludgeon and Seaspray (purely because they belong in the Classics line)
Masterpiece - US & JP - Masterpiece Magnus (he's not really ultra without his trailer).