I wouldn't consider them emotional as they were just attention-grabbing. Everyone would have reacted differently. Sniper Wolf's death would have been emotional for me had she not been a royal pain in the ass as far back as the first time she shot Meryl.
So yeah, I think I felt the most emotional over Meryl being in pain because she was such a rookie in the field. You hate to see the greenhorns take a dive and she just had so much shit in her life to deal with prior to Shadow Moses. The first time I played through MGS1 on PSX, I gave up during the torture chamber and they killed her and I'm not one to reload save data if I fuck something up. I let it ride, makes that play-through a unique experience from any future ones.
Naomi and Grey Fox's little schtick was the next saddest for me. Beyond that, I was more or less caught up in the intrigue and conspiracies behind the entire Shadow Moses incident.