The sets are: Premier the first released set; Alternate Universe the second released set; Q-Continuum the third released set; and First Contact the most recent set, save The Fajo Collection which, as I said, is a limited edition set with only 40,000 copies. The Fajo Collection sells for $80, but you can pay as little as $50, if you have three $10 off coupons from the ST:CCG First Anthology (which contains 2 premier starter packs, 2 premier booster packs, 2 Alternate Universe packs, 2 Q Continuum packs, a Warp Pack*, and a pack of Star Trek: Voyager and DS9 preview cards, available only through the anthology and trading).
*A Warp Pack contains previews of cards that, when it was initially released (as a free promotional offer), contained cards to be released in a later set (although you can find them in the Alternate Universe set now).