Most of what's online at the moment in terms of comics tends to be previews of current titles rather than full issues or story arcs. The Japanese mangas from the 80s are definately online somewhere, I'll try to find you a link for that shortly. First off a bit of an overview of the various G1 comics from across the years, since there have been quite a few.
Transformers (Marvel US) ran for 80 issues with 2 writers first Bob Budiansky who wrote the personalities and abilities of the original TFs from 1984 and later Simon Furman who has written more TF fiction than anyone else in the business. The initial stories told of the TFs coming to Earth and adapting to their new environment. The continuity differs from the cartoons with details such as why the TFs left Cybertron being different, the Dinobots being members of the Ark crew rather than built on Earth and so on. New characters were introduced over time as various new toys came out, the main exceptions being the main cast of the 1986 movie who were not touched on at the time although some did show up in the Headmaster related material and later material written by Furman. The origin of the TFs is tackled by Furman in his stories and this is probably the biggest break from the cartoons. Here the TFs are the children of Primus, last of the gods of light, created as a final deffence against Unicron, last of the chaos gods. Quite a major departure from the cartoon backstory that the TFs were made by the Quintessons before they were driven from Cybertron. The final story arc dealt with Unicron's defeat at the hands of the combined Autobot and Decepticon forces.
Transformers Headmasters (Marvel US) 4 issue miniseries that fits within the 80 issue run above and introduced the Headmaster characters on the planet of Nebulos before they journeyed to Earth and joined the cast of the main story. Both of these books and the Generation 2 comics (more on these in a little while) were collected by Titan Books a couple of years ago adding up to around 16 volumes of material.
Transformers The Movie (Marvel US) 4 issue miniseries adaptation of the 86 movie not tying directly into the main run of marvel comics. Adapted by Budiansky this story has recently been redone with additional scenes and completely updated art by IDW Publishing.
Transformers (Marvel UK) 326 issues varying between fortnightly and weekly, both reprinting US material and producing new stories. Initially the UK originated material had to fit inbetween the US reprints but as Furman found his feet this took off on some tangents and deviated from what was being done in the states to a larger degree. Furman used the movie cast that the American comic wasn't utalising and set a lot of his stories in the future (well 2005 onwards, so the past to us now, but I digress) with time travel elements linking back to the main continuity. It was in these future stories that the concept of Primus was first introduced allowing Furman to introce it again in a contempory setting once he was writing for the US book. A lot of the UK material has also been collected in book form by Titan.
Transformers Generation 2 (Marvel US) 12 Issues picking up the story some time after the original 80 issue run. It's a direct continuation and a cracking read so I thought I'd better mention it.
Transformers The War Within (Dreamwave) 3 6 issue arcs (the last arc never finished due to the compasny going out of business) set in Cybertron's distant past. Written by Furman and highly recomended. This is where the pre earth designs that have been featured in the recent Titanium toy line originated. Completely seperate to the Marvel comics these stories tie in with Dreamwave's G1 continuity.
Transformers Micromasters (Dreamwave) 4 issues set between the War Within books and the main Dreamwave G1 continuity, after Prime and Megatron have left Cybertron but long before their reawakening on Earth. Focusing on the newly created and anarchic Micromasters characters these comics tried to evoke a more 'punk' sensability than is usually found in TF fiction.
Transformers Generation 1 (Dreamwave) 2 6 issue arcs and an ongoing title that made it to 8 issues before the company disappeared. Drawing influence mainly from the cartoon and in theory filling in some story from between the end of the second season and the movie. The later stuff was basicly building up to retell the movie story. Most of the Dreamwave material has been collected in book form at some stage and IDW have some of it still in print, although there are various legal difficulties with the rights to some of this material.
Megatron Origin (IDW Publishing) 4 issue mini, currently being published. Sets up some backstory to the totally reimagined IDW continuity for G1.
Transformers Infiltration, Stormbringer, Escalation, Devastation, Revalation etc (IDW) Mainly 6 issue arcs (Stormbringer is 4) telling the contempary TF storys in the new IDW continuity. Written by Furman these are quite intricate and interlinked across the IDW G1 titles with lots of subplots and things being set up to pay off storywise somewhere down the line. The first 3 arcs are already out and should all be available as collections soon if not already, the last couple (and more beyond) are forthcoming.
Spotlight titles (IDW) These focus on a specific character telling a story within a single issue that links in to the main IDW continuity without having to distract too much from the main story thrust of the (...)tion titles. Mostly written by Furman.
There are other bits and pieces out there, GI Joe crossovers and suchlike but I think that's most of the main comic continuities that you might want to give a look. I'll see if I can find that link to the manga for you now.
edit- Here we are:
http://tfarchive.com/comics/japanese/
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