The BBC recently did a study on the portrayals of LGBT characters in TV, and came to the conclusion that such roles need to be diversified beyond simple "gay" storylines. Much praise went to Doctor Who, which has always been extremely astounding when it comes to treating LGBT characters as, well, characters and not stereotypes. That being said, look for my upcoming article "10 Most Tacky Gay Jokes in Doctor Who."
All kidding aside, you really have to give the show credit for the way it will allow a character of non-hetero persuasion to act normally with that aspect of themselves being simply another trait. The bi or omnisexual Captain Jack Harkness is the best known example, being a lighthearted horn dog, a troubled immortal, and a pragmatic soldier all at the same time. There are plenty of more minor and casual players, like Vastra and Jenny, Lady Cassandra, and the Cassini Sisters, and the fact that they drop in and out of episodes so seamlessly is testament to Doctor Who's status as a bastion for realistic LGBT interactions on television.
It did make me wonder though... how does one classify the sexuality of the Doctor himself?