There are quite a few different continuities from over the years and while they may not all agree with each other all that much or at all they have all been produced under license from Hasbro so can all be considered canon to some extent. Check out my post here:
http://seibertron.com/forums/viewtopic.php?t=10200&sid=For a breif overview of the different takes on G1 from across the years with some notes on what's been collected into book form.
As for the best place to start my personal recommendation would be the IDW books, beginning with Infiltration. It's a different take on G1 than anything that's been done before but as it's recently published and currently ongoing material it's easy to find and the writing is really multi layered with different strands linking from their various titles back to their core books more and more as you get into it.
If you're hankering for some more 80s cartoon themed stories then the Dreamwave titles from a few years ago fit the bill. Be warned with these however that the writing can be quite 'fanish' and that the series just stops mid story due to the company going out of business. The War Within books from Dreamwave I would recommend above the rest of their output.
My main focus is the G1 books, but I've read most titles from other continuities as well, so feel free to ask specific questions about any of those, but I sort of gathered from your post that you were mainly thinking about G1. Hope that helps.