Who are your favourite side character NPCs?

Well, to the writers' credit, keeping these creatures out of the limelight and from becoming familiar helps keep their alienness, though more could have been done for sure. The Thorian for one could have had more screen time, maybe as a living off-spring, embedded in a host, seen in ME2 or 3.

And would have been interesting when comparing against the Leviathan, and why the Reapers didn't go after it. Which, to me, is probably one of the larger holes in the lore. Not that it was necessary to close, since the Thorian didn't try going off-world. It just would have been interesting to see the cross-referencing of the two species.

Emily Wong > Khalisa

I also liked the Rachni and their Queen. One of the more interesting alien species in Mass Effect.

Gianna Parasini and Conrad Verner.

Matriarch Aethyta, Gatatog Uvenk and that Elcor bouncer in front of Afterlife.

Yeah that was why I liked her from the start. Great character. She would be an excellent drinking partner I think. Lol

Lorik Qui'in from Mass Effect 1. The guy was just fun to talk to and persuade into doing stuff.

Kate Bowman from "Bring Down the Sky". Competent and courageous, Cyrus Shepard felt she was the kind of person for whom he saved the galaxy, unlike so many others he met in the course of his life, but as she didn't survive, he'd always feel he failed her. She was the kind of person he'd see in his dreams in ME3.

Honorable mention:
Gianna Parasini
Aethyta
Brynn Cole

...and quite a few others. I sometimes feel the ME team did better with their small stories than with the big one.

Han Olar, the painfully sane Volus on Noveria.
Detective Anaya: I felt she was good at doing her difficult job in an immensely difficult situation. Anaya was just a regular cop, trying to keep the peace until Samara and Shep dropped on her.
Shiala
The Elcor ambassador, Kalyn? on ME1, the one who tells Din Korlak to stop being rude. I be fair i like all the Elcor. Andromeda needs Elcor!
I actually quite liked Lizbeth Bainham, i like that she's still apologising for shooting at Shep in an email in ME2.
LOVE the "Prothean no like you!" Vorcha.
Does Eve/Bakara count?
I do quite like the rachni queen, I must one of the few people who find her talk of colours oddly poetic. I feel quite bad about slaughtering ever other rachni I come across.
The salarian guys you can save in Thane's recruitment mission. "Tell your assassin to aim for her head, because she doesn't have a heart." (or words to that effect...) I can't remember if he's the same guy who has the nervy gung-ho brother, or the one Shep tells "You should go."

Also his armour is just...no.