I'd say that my favorite was Mimura, since he had a calm head throughout everything that happened. And even though his guts were spilling out and his foot was shot off, he was still able to detonate the bomb. Adding to that, even on the verge of death, he had a back-up plan (the "clutch shot").
I also hated Froggy the most. I can sympathize with some of what he says, like when he points out that as a violinist, he got forced applause whereas Shuuya got scream and cheers when he played the guitar. I really couldn't get over how egotistical he was just because he was lucky enough to be born into a rich family.
I felt sorry for Hardcore Souma. She's a criminal, sure, but it's not her fault. The insight on the relationship with her father towards the end was really tragic, especially how she still loved him and wanted to help him after he all he had put her through. Her demise was really tearjerking, because even in her final, delusional moments, she's still craving her father's love. It really pissed me off how Kiriyama didn't just put her out of her misery but instead blew the ring right off her hand.
I can relate to Shougo most. It's funny how at the beginning of the story, I thought to myself that Shuuya should try to eliminate everyone but Noriko and then off himself to let Noriko live. It just happens that Shougo had planned to do the same in the first Program. I also understand his desire to stay hidden and avoid attention, even if it may save some people's lives.
I felt Yoshi should have survived. He was the shy, innocent type and did nothing more than stand up for people and got killed. But killing off such an important character early on gives you that sense that it not just some typical manga plot where the good guys all survive--instead, it shows you just how real this game is. People are playing for their lives, not for your reading entertainment.