Heheh, you just opened Pandora's box... ;)
Essentially, the Dreamwave comics are in their own continuity, based on elements of both the US cartoon and the Marvel comics (but primarily the cartoon). The DW material frequently attempted to create the One True Unified Continuity, and was (for a time, at least) regarded as the new 'official' continuity by Hasbro.
As to the other series, it runs something like this:
US cartoon continuityG1 cartoon S1-2 -> TF: The Movie -> G1 cartoon S3 -> The Rebirth
Cartoon -> Beast Wars -> Beast Machines
The cartoon -> Beast continuity is generally accepted, though not without exception.
Japanese cartoon continuityG1 S1-2 (Fight! Super Robot Lifeform Transformers) -> G1 S3 (Transformers: 2010) -> Transformers: Headmasters -> Transformers: Super God Masterforce -> Transformers: Victory -> Transformers: Zone -> various manga...
Scramble City bridged the S2 to S3 gap in Japan until they eventually got the Movie.
(I'm not certain how the Japanese dubs of Beast Wars (S1) / Beast Wars Metals (S2/3) and the Japanese-exclusive shows Beast Wars 2 and Beast Wars Neo fit into the Japanese cartoon continuity, or whether they're a separate entity in their own right.)
Marvel continuityMarvel US #1-80 -> Marvel US G2
Marvel UK #1-#332 interleave between the US stories without too much trouble.
The Marvel adaptation of TFTM is outside of the regular comic continuity; the appearances of Unicron, Galvatron
et al in the Marvel continuity generally involve time travel and/or alternate universes.
The UK G2 comics are generally ignored due to being, well, pretty crap really.
Various prose stories penned by Simon Furman for conventions are retroactively included in the G1-G2 comic continuity as well.
Dreamwave continuityPretty much everything Dreamwave published, including the DK Ultimate Guide. The G1 continuity received a reboot which tried to tie together the existing comic and cartoon continuities whilst inserting some of its own material. There is particular confusion over the 'Original 13' element of the G1 history, which AFAIK is
similar to but intended to replace the 'Original 12' and Omega Point elements of Furman's retcon convention material.
The Unicron TrilogyArmada -> Energon -> Cybertron (Hasbro version only)
The three recent series are in their own continuity (in the Hasbro dub; Galaxy Force, for example, had no links to Energon in the Japanese original). They make allusions to earlier G1 material, but this should be understood as an 'alternate universe' version of that material.
IDW comicsBeast Wars: The Gathering (and any sequels) are in the US Beast Wars show continuity, with additional elements drawn in from the Japanese shows.
Hearts of Steel is a what-if standalone continuity.
Infiltration, Escalation, Devastation, Stormbringer, the various Spotlights and the Megatron origin, along with anything else in the G1 universe, is all set in a single, newly 're-imagined' G1 continuity.
Other stuffUh, I think pretty much everything else falls under 'what-ifs' and standalone continuities. TF: Universe is the main player here, being in itself an amalgamated continuity pulling elements from all over the place (read: any toyline with a repaintable, marketable mould available).
That probably muddied the waters for you, but I hope it helped a bit!
--EDIT--
For reference, this would have been the first reply if it hadn't taken so damn long to type!