I've played every class to a pretty high level now and I'm starting to get a feel for the various companions in the game.
I don't know how you guys tend to favor companions, but when I stumble on a companion I really like, they become my one and only. Doesn't matter if it's a companion that completely breaks my class, I just want to use that companion so I can get as many dialogue options as possible throughout the missions.
As such, I've found some favorites for each class, but I also think I'm able to narrow it down to an overall favorite:
I know Kali is getting a lot of flak on the (other) forums because of her completely insane personality, but I really like the character. She's spunky, like Kira and Vette, but she's not the goody two-shoes they are, and yet it's still easy to go Light Side with her, you just have to not be a complete tool all the time. She's very sarcastic and she loves it when I don't run off and kill myself for no good reason, unlike other companions who encourage me to do just that. More than once.
Kira and Vette are among my favorites as well, primarily because they're also sarcastic in their behavior. I guess my main attraction to Kali over Vette is that Vette, in my mind, tends to roll her eyes more, whereas I imagine Kali delivering her lines with a flirtatious wink. Vette is cute, but Kali is just damn sexy! Kira is like a mix between Vette and Kali, but like Vette, she has a tendency to be almost juvenile in her behavior. She's also on the other side of the fight, so she gets to be my number one Republic companion.
Who's your all-time favorite?