Essential:
War Within Volume 1
More Than Meets The Eye (not a comic story but worth it)

Other comments:
War Within Vol 2 is not as good IMHO, and Vol 3 ended when the series got cancelled.

Dreamwave's first G1 series was pretty rubbish, the second improved, and I think the third was excellent (but it built on the first two so if you went there first it might not make much sense, and it ended with cliffhangers when the comic got axed so it's a little harder to recommend)

Micromasters was a skippable mess.

Armada/Energon was enjoyable, better than the cartoon, but also got cancelled midstory. The "Worlds Collide" four parter was the pick.

IDW's series are very complicated that it's hard to read just some of it, but I think people might recommend Stormbringer, which is not bad. The Devastation series is my favourite.

However, some of the spotlights are worth picking up by themselves: Kup, Ultra Magnus, Shockwave, Ramjet, Soundwave (and Wheelie but I know most people hate the character and that might put you off too).

Hearts of Steel had a good idea (TFs wake up in the 1800s) but was poorly executed.

The Beast Wars comics might appeal to you f you like the Beast Wars toys.

In the Movie comics The Reign of Starscream Movie series was probably the best.