Last I saw (Deathtrap) Vigilante took out his eyes. Then, when I'm reading the Blackest Night tie-in for Teen Titans, we see his eyes back. What happened? Did I miss something?
 
Also, why isn't he mute anymore? I thought that was weird when I was reading Deathtrap.

The Specter?

He was mute because his vocal chords had been damaged as a child.  When the souls of Azarath housed themselves inside his body, it granted him a healing factor and his throat healed and he could talk again.
 
After his death, he was given a new body in the same fashion that Raven got her new body.  So even if his throat hadn't heald, he would still have had a brand new one along with his new body.  Why he never spoke after being brought back was never explained, but when they chose to make him a villian they decided to take advantage of the fact that there was no physical reason why he shouldn't talk.
 
Also I agree that it is really stupid that his eyes would just grow back on their own.  Not only does it not make sense, but it was a cheap fix and made the end of Death Trap completely pointless.
 
Maybe we'll get a better explanation, but I imagine we probably won't hear much about Joey for a while.

I just read the character history and he was brought back by the regeneration matrix made by Deathstroke and Dr sivana. Which also brought back his ability to talk.