After my eighth replay of Mass Effect 2 (straight from ME1), I will say my favorites have shifted a little bit.
Male:
-01. Jacob Taylor- best looking male LI, level headed soldier, and is actually not a pain in the rear. Comes without baggage and has them abs.
-02. Thane- wasn't my initial favorite but this guy's really growing on me. Will probably do a Thane-mancer the next Fem Shep I create. Especially with the DLC alternate appearance, he's that much more of a bad-a**
-03. Wrex- Very funny in Mass Effect, love his commentary and how he grows as a character. He doesn't stop being a bad-a** but is the type of bad-a** that is tough for his people and loyal to his friends.
-04. James Vega- I don't know him well yet since ME3 isn't out, but I can appreciate from what little I do know, he at least looks like a man, ACTS like a man, and it's always nice to have a tough as nails soldier boy.
-05. Garrus- He's grown on me...I still think he's pretty boring in Mass Effect 1 and probably one of the least useful, but he comes into his own in ME2. Still I don't plan on making him an LI for any of my Sheps...that's just too weird.
-06. Kolyat- He may have a small role but he's one of those characters I'd really like to find out what happens next to him and what the future holds. I'd like to see him return in Mass Effect 3, if nothing more than to be a cameo that helps or hinders you depending on your choices. Would be cool to see him aid his father on Invictus.
-07. Turian Councilor- He's such a jerk that forces the player to hate him so much that...I actually like him. Well written character...actually lol'd with "Ah yes...'Reapers'...". He's just one of those NPCs you love to hate...and reluctantly love him because you hate him so much.
-08. Kal Reegar- Tali's not the only cool quarian. Love the voice (strange how he doesn't have the Eastern European accent) and for a small role NPC he's pretty awesome. Would love to see him again for ME3.
-09. Kaidan Alenko- Despite being a total douche on Horizon...he was actually my first LI the very first time I played Mass Effect. He still cares (for FemShep) and I'm dying to see what happens when he becomes a Spectre. A bad-a** Kaidan? Bring it on!
-10. Mouse- One of the few male NPCs that's actually really good looking. Wish I could upload his face to my Shep. Had a real small role and didn't do anything newsworthy, but makes the list merely because he looks good. Babyface ftw.
Females:
-01. Jack- Most awesome female squaddie. She's not conventional, she doesn't worship the ground Shepard (male or female) walks on, and she remains herself even after you romance her.
-02. Samara- Used to be my first favorite but Jack took her place. Still, an asari palad- I mean justicar, is pretty awesome. She's elegant, beautiful, and love her voice. I'm not the type that wants everyone in the game as an LI...but she would've made an awesome one.
-03. Kasumi- Finally broke the Bioware trope female...she's not a redhead or dark haired European chick nor is she someone with insecurity issues. Ninja + Thief + Japanese + Happy go lucky attitude + Daredevil + Individualist + doesn't develop an interest in Shepard past a professional relationship? Sounds like a realistic, awesome squaddie to me!
-04. Fem Shepard or My Canon Shepard- She counts in the ME Universe...she's just pretty awesome. A strong female protagonist that affects the universe and isn't merely a man with female assets. Plus Jennifer Hale voices her. Doesn't get better than that.
-05. Morinth- Actually found her more compelling after my latest playthrough. It's too bad it's pretty hard to get her based on your diplomacy level, but she's pretty interesting as a character. Basically a tragic character that's driven by her impulses...you can really see it during her confrontation with Samara.
-06. Gianna Parasini- Pretty, classy, and always on the go. One of the coolest female NPCs of Mass Effect.
-07. Emily Wong- Another cool female NPC. Would love to see her punch Khalisah instead of Shepard.
-08. Matriarch Aethyeta- Love her voice...she needs to bartend for the Normandy...in Kasumi's bar.
-09. Matriarch Benezia- One of the most awesome female villains encountered in Mass Effect. Also one of the most fun boss fights because her biotics are such a pain like that.
-10. Miranda- She gets a spot merely because she's the most useful squaddie in Mass Effect 2. Admittedly I like her less than I used to but she's still got her awesome moments. But Jack tops her anyday!