Samaras by far. One of only a small handful of moments in the ENTIRE GAME where it actually said "Ive got a great idea! Lets not just simply revolve around dumbed down shooter combat, but try something different!"
Thanes was another good one. Talis loyalty mission started well by went downhill, especially when the migrant fleet is summed up in game by one pathetic "open hall" and following that another one of the games many trademark linear shooting galleries. It was just pathetic...
Most of the others were crap, just constant waves of enemies broken up by short conversations either trying to make the cast appear "cool" or trying too hard to be "emotional".
Mordin, while a great character, has the most overrated loyalty mission by far. Hes a well written character, but his loyalty mission is a) simply restating most of what is known already. For someone who hasnt forgotten all about the genephage, it was boring. Also, b) it was a ridiculous "damned if you do, damned if you dont" argument, just like the original use of the genophage. Blood was on Mordins and every other persons hands no matter what, even the krogan, both in the beginning at when his team worked on the genophage.