The Apogee was significantly stronger when you got bonus damage from high flux. However, it's still a good ship even now. (The reason I've started using a Dominator instead? It can also take on most things, and it costs significantly less supplies to deploy. The Apogee is still more durable, though, and fares better against frigate or fighter swarms.)
My current favorite configuration uses 2x heavy blaster, an autopulse laser, and 2x tactical laser in the turrets. Yeah, doesn't focus fire well... but it doesn't need to; you burn through most of the autopulse's charges, then rotate to bring a heavy blaster to bear, and do it all from extreme range where most things can't retaliate effectively. (The tactical lasers are only there to help against fighters, really.)
You will, of course, want ITU and augmented engines and stabilized shields and combat 10 for extra speed & shield strength & weapon speed (useful for making heavy blasters able to hit fighters reliably).
You can only get both heavy blasters aimed at a single target if it's something big - generally cruisers and up - but that's okay; even just one heavy blaster is plenty of DPS against any smaller targets.
I wouldn't take it up against a combat-10 Onslaught, but anything else goes down without much trouble.
Plasma Cannon sniper used to be a pretty good use of an Apogee, too, but the plasma cannon is much less potent now than it was; this is still doable, but it's not quite as powerful a build as it used to be.
For me, the Apogee was tier 1 - overwhelmingly potent against almost anything - and is now tier 2.