Kaidan - The only romance I really enjoy in the series, and one of the few I have any interest in completing the subplot. Also, I find his support biotic abilities like reave realy useful, since my characters tend to be more offensive.
Garrus - Any doubt he would be here? The man is simply awesome and the best bro you could ever have.
James Vega: Yes, is not the first nor the last unpopular character in my list lol He is the stereotypical beefy dude alright, but I just like having him arround because I like the mentor thing he and Shepard have, and making fun of him is always amusing.
Tali - She is adorable. Keelah Se'lai. Enough said.
EDI - Loved her in Me2, and continued to like her in Me3. I just wish they didn't turn her into a sexbot to make her a companion.
Moridn - I am the very model of a scientist salarian, I've studied species turian, asari, and batarian.
I'm quite good at genetics (as a subset of biology) because i am an expert (which i know is a tautology).
My xenoscience studies range from urban to agrarian, I am the very model of a scientist salarian..... *clears throat*
Thane - Ninja/assassin and free from that "I'm too cool for you" atitude that I absolute hate? Win. Plus, the whole thing with his son and the terminal desease is really moving.
Miranda - It's funny, I thought I would despise her based on her first appearance, but she didn't just grew on me, she became one of my favorite characters. But just a note for the future bioware: You don't need to have a character's ****** and ass on screen EVERY time she appears to make her sexy. It's very hard to take Miranda seriously sometimes, especially wen she is trying to advise me about some critical mission or talking about some problems with her family if half of the screen is covered by her fat ass ._.
Samara - Yeah yeah, I know most people find her boring because her personality is completely subverted by her code, and while I do wish we had seen some vulnerability and seen the person behind the justicar more, I still think she is a badass and I enjoyed having her as a companion.
ME1 Liara - Emphasis on ME1. I really found amusing how much of awkward bookworm she was. She was so nerdy and shy, I just enjoyed having her around, and the little crush she developed for my Shepard was adorable, even if him wasn't interested in her that way. A shame that they changed her character completely in ME2, and I dislike everything about her since.
Kasumi: Most well spent money in a dlc in the saga. Me2 without her is so boring.
Wrex and Gruth: Because you can't have enough Krogan in your life lol