The first two major Trek games that I played on PC were Armada and Elite Force.
Armada was a decently made RTS, though the single player was far stronger then the multiplayer, but even MP had its moments.
The game tied together many elements from the series, The dominion war aftermath (DS9), Insurrection, The Omega Particles (VOY) and the Borg. The voice acting by Patrick Stewart (Picard and the cloned Locutus), Denise Crosby (Sela) and the dynamic duo of Michael Dorn and JG Hertzler was top-notch. The four campagns tied together reasonably well.
Elite Force (made by Raven (SW:JKII)) was its sister game, set in the Voyager 'verse. Again, single player was unique (the first real Trek shooter), with a storyline that actually 'fit' Voyager (the opening 'mission' was a clever bit IMO), and actually made more sense then what happened in the show itself in the later years (sad, sad). multiplayer was the only downside, as the game used the Quake III engine, MP was basically Q3 with Trek skins.
Since then, meh.