There is probably a page with this info, but I can't find it. The question is: Is there a compilation of what energy types are most (or least) effective against the various races? I know the obvious ones: Synchronic proton for Devidians, sonic AP for Tholians, cold (CRM200, compressed cryo, etc) against Tholians and Gorn. Is there a general rule that a race's own energy type is not very effective against them (e.g., cold vs. Breen)?

well the cryo (cold dmg) is most effective against all species and in PVP except breen.
But i doubt there is a list of the resistances of each species.

There's no particular vulnerabilities, really.

Tholians aren't exactly weak to sonic weapons, those weapons just have a special proc that only works against Tholians. There's similar weapons from the STF vendors that do additional kinetic damage to Borg. Those weapons give up one of their bonuses for those procs, too, so it's not a pure gain.

The Proton rifle is a bit odd - it's only the alternate fire that's effective against Devidians, and only when they're phase shifted (went they go transparent). It also works against players who are phase shifted by a triolic pattern enhancer. They get a boost to antiproton defense (as well as everything else) while phase shifted, too, so they resist the weapon's primary fire at the same time.

In other cases, resistances are either approximately even across the board (Borg don't resist plasma any more than they resist anything else), or pretty small (Breen don't resist cold enough and Tholians aren't vulnerable enough to it to make a significant difference). Borg adaptation is an oddball case - having two different energy types helps a lot, but it doesn't really matter what types either one is.

Not sure what they have done but the Sonic Antiproton weapons do absolutely no extra damage whats so ever to the Tholian's.