In the book, the end of the chapter where Neville finds the dog. After spending a month trying to get the last living creature on Earth other than himself to allow Neville to pet him, it finally looks like he will have a companion. It'll be easier just to read it yourself:
"You'll be all better soon," he whispered. "Real soon."
The dog looked up at him with its dulled, sick eyes and then its tongue faltered out and licked roughly and moistly across the palm of Neville's hand.
Something broke in Neville's throat. He sat there silently while tears ran slowly down his cheeks.
In a week, the dog was dead.
Virginia returning from her grave. And then few chapters later Neville tearfully tells Ruth how it feels to stake your own wife and how much effort it takes to convince yourself she's no longer the woman you love.
During the flashbacks, an infected mother can be seen begging for her daughter to be taken to safety in the middle of the chaos to leave Manhattan.
When Sam gets infected whilst saving Neville's life and he's forced to Mercy Kill her. Not only did he lose his only companion of the last three years, but also one of the last remaining links to his family at the same time.
In the movie, the aforementioned Shoot The Dog moment, and the moment Dr. Neville begs the mannequin to say hello to him, since he had promised Sam he would try for it.
Who didn't tear up during the climax of the film, especially when he tries negotiating with the infected trying to break down his door moments after he finds the cure, desperately hoping to get through to them and prove that the last three years and all his suffering haven't been in vain.
Neville: Look, look, look, I can save you. I can-I can help you. You are sick and I can help you. I can... I can fix this! I can save everybody! I can fix everything! It's working. It's working! Stop! Stop! I can save you! LET ME SAVE YOU!!!!
For that matter, the original climax. While there's ultimately a happy ending for everyone, the male Darkseeker's grief, fury, and sheer, broken relief are all extremely palpable. Throw in Neville's My God, What Have I Done? moment and it's powerful stuff all around, especially when the Alpha roars and it immediately transitions to the wall full of dozens of Darkseekers Neville killed while looking for the cure.
Neville: ...I'm sorry.
The "Look Daddy, a butterfly" line right before Dr. Neville's demise and the death itself.
''Isolation’’: Written form the Perspective of an infamous Super Max inmate that was left to die alone in prison. He escapes, only to be hunted down and backed to a corner by the Darkseekers, the last minutes reveal he was a Moral Extremist who engaged in acts of Domestic Terrorism. The last frame is of him preparing his last stand as the darkseekers close in on him. Despite the man’s crimes, it would have probably been more humane to just put a bullet in the guys head over just letting him dehydrate and starve to death alone.
What’s worse is that in the end, after pumping his shotgun, only one gunshot is heard, hinting that he actually took his own life rather than be mauled to death by the Darkseekers.
A tie-in promotional piece depicts a camera crew's experiences in Manhattan on the night the city was quarantined. Near the end, the reporter begins to visibly break down from the chaos ensuing around her while she tries to maintain her composure and continue to do her job. She eventually collapses into total despair, tearfully lamenting about how the end may have finally come for humanity.
