Ahh, the loyalty missions were excellent in Mass Effect 2. But which was the best, hmm...
I've gotta say Jack's, because it really reveals a lot about her past and it actually seems like she's worse off for it, despite being grateful to have it out of her mind.
Samara's was memorable, I'll give it that. I don't think it was the best because I find her less interesting than Jack, but goddamn that mission ends on one hell of a high-note. Interestingly, I found the mission to have a lot more impact on my second play-through. Maybe I felt more sympathy for them once I knew everything involved?
Kasumi's started and ended on high-notes, but I wasn't a fan of the combat sections of it. Really well done end choices for her, in my opinion. Really felt for the poor girl
Wasn't a fan of Garrus' though. Not sure why, I think I just don't like the drawn-out combat with the Blue Suns in it. It felt so unnecessary.
On an overall note, I loved how the choices you made in the loyalty missions build on the characters for potentially huge personal struggles in the future. I really hope Bioware takes everything into consideration to give the appropriate consequences.
EDIT: Also, Liara's is pretty awesome if that counts. It's just a shame it feels like a 2-man squad with a third wheel.