The weapon 'balance' is pretty much 'missiles and then everything else', yes. The main caveat is that you will, at some point, run out of ammo - either on the frontlines, or if things are particularly bad, even in your planetary stockpiles. Once a beam weapon is built, it costs nothing to fire it, so you'll want both.
As far as the beam weapons themselves go, the easiest, newbie-friendliest is probably lasers. The same tech lines get you solid offensive and defensive weapons, though they aren't 'the best' at either.
Of the remaining weapons, particle beams (for steady damage at range), gauss cannons (for high rate-of-fire vs. incoming missiles), and mesons (for ignoring armor) seem to be quite popular. Microwaves, as I said, are a supporting weapon at best. Plasma carronades are sort of the black sheep, having no real advantages beyond doing more damage for the same amount of research. Railguns are sort of a mix of several different weapons, but are still fairly middle-of-the-road, like lasers, except they can't be turreted so aren't useful defensively except for the fact they can fire four shots at a missile.
