I don't think Mercer was gay; I think there have been several subtle hints that Beckett was at least bi-sexual, though. The way he he spoke to Jack, the rather homo way of waving that damn fan, the mysterious nature of the "mark" Jack left on him [which was never resolved, damn it], and that really small... gun.
...That said, Beckett and Mercer are still badass villains. Beckett and Mercer remind me of Emperor Palpatine and Darth Maul from Star Wars. Beckett is the more evil of the two, but - like Palpatine - he's not always engaging in evil acts. He's polite, sarcastic, and manipulates others more than outright slaughtering them. Mercer, on the other hand, is always engaging in some sort of villainous act, he's a man of little words (like Maul), and he's pretty much dedicated to his master's cause. They were a really good evil tag-team and I wished more was explored.
But Mercer, to me, is the ultimate evil henchman. Vader and Maul can kiss my ass. The way he shot that Asian twin, and her sister gave Mercer the 'I'm-gonna-kill-you-painfully' look. Then later it shows him pulling a metal chopstick from his shoulder, standing victorious over the surviving twin, before shooting her. He was also in a position to kill Will Turner, he put DAVY JONES back in his place, and stood toe-to-toe with Barbossa.