I decided to make a new thread having a (recommended) reading list for the series. Take note that one of the biggest contributors to the TF series is Simon Furman, and as such I will try to provide what comics he wrote.
Marvel era:
I don’t know if this series is even collected, but there are 2 continuities: the US and UK. IIRC, UK lasted a little longer than US. Furthermore, Simon Furman would write the US comic from #56-80, so if you’re issue hunting you may want to get those.
If you’re living in the UK, you may want to look into these-
http://titanbooks.com/search/all/?search=transformers&type=Book
As I’ve heard that they have collected some of the 80s TF comic series into TPB.
Dreamwave era:
I haven’t read much of the DW comics, and any that I did I had done so long ago ^_^; …but after doing some quick research, Simon wrote for the Armada and Energon comic series, so see if you can get those (even if you didn’t like the shows, it may be worth reading them due to Furman’s input).
Dreamwave did publish a comic based on the Generation 1 series, but set in an alt. future and are collected in TPB-
http://www.amazon.com/Transformers-Generation-Graphic-Novels-Vol/dp/1933239824/ref=sr_1_3?ie=UTF8&qid=1306358110&sr=8-3
The Gen. 1 comic did have a 3rd volume but I can’t seem to find it in TPB
Another series Simon Furman wrote for Dreamwave is one that took place on Cybertron during the War, by the time Dreamwave went bankrupt, only 2 story arcs were completed with the 3rd one having only 3 issues published =( Non the less the first two are available in TPB-
http://www.amazon.com/Transformers-War-Within-Pocket-Paperback/dp/1897105010/ref=sr_1_1?ie=UTF8&qid=1306358398&sr=8-1
The 2nd book is War Within: The dark ages, which doesn’t seem to be collected in TPB format I guess?
G. I. Joe crossovers:
There were 4 TF and G. I. Joe crossover series released, during the 2000s-
http://www.amazon.com/Transformers-G-I-Joe-Vol/dp/0973381795/ref=sr_1_9?s=books&ie=UTF8&qid=1306358560&sr=1-9
http://www.amazon.com/G-I-Joe-Transformers-Graphic-Novels/dp/1932796320/ref=sr_1_11?ie=UTF8&s=books&qid=1306358651&sr=1-11
http://www.amazon.com/G-I-Joe-Vs-Transformers-Graphic/dp/1932796649/ref=sr_1_1?s=books&ie=UTF8&qid=1306358675&sr=1-1
The 4th book was titled Black Horizon and was only 2 issues, so I don’t know if it was collected.
IDW
After Dreamwave went bankrupt, IDW picked up the TF license and has been publishing the series since then. One thing most might have trouble with thier series is the reading order as one will need to read Spotlight issues to get some additional background info on events. I’ve provided a recommended reading order which is based on chronological event, but giving priority to main series…unless stated otherwise:
0- Megatron Origins
1- Spotlight Vol. 1 and Infiltration
2- Stormbringer (events take place before Infiltration, however Infiltration was released first)
3- Escalation
4- Spotlight Vol. 2
5- Devastation
6- Spotlight Vol. 3
7- Revelations (this would be the conclusion to Simon Furman’s main run on the TF books as much, if not all, of what he had written in the books prior to this one come full circle…albiet in a rushed manner)
8- Maximum Dinobots (this was written by Furman and resolves one plotline that was not featured in Revelations)
9- All Hail Megatron Vol. 1 (This was intended as a starting point for newcomers and was written by Shane McCarthy, who used and dropped some elements from Furman’s run. If you read Furman’s run then go into this you may notice how out of place it’ll feel)
10- All Hail Megatron Vol. 3 This is actually a collection of Spotlight issues, you could either read it inbetween or after Vol. 2
11- All Hail Megatron Vol. 2 and then Coda (AHM Vol. 4)
12- Drift (IIRC this details his origin and takes place BEFORE AHM, you don’t need to read it first though)
12- Last stand of the wreckers
13- The new ongoing titled Vol. 2
17- Bumblebee (takes place after the first book of Vol. 2)
18- Ironhide
Finally, Simon Furman wrote 2 **Beast Wars **miniseries which take place during and after Season 3 of the show, the first book is called The Gathering, followed by The Ascending, and are collected in this omnibus if anyone wants-
http://www.amazon.com/Transformers-Beast-Omnibus-Simon-Furman/dp/1600103901/ref=sr_1_2?s=books&ie=UTF8&qid=1306359925&sr=1-2
Note that this book features characters that were not used in the cartoon due to budget limits and all that, as well as other toys made for the BW toyline.
Oh and the Avengers crossover…wasn’t very good, despite the fact that it may be considered canon!
As a final note, most of the TF series tend to star characters that otherwise would’ve been ‘guest characters’ in the cartoon, for example in Stormbringer the main characters include Jetfire and the Technobots.
Hope this helps and feel free to ask for additional info.