Money
When Robert is searching for Sam in a building full of the infected we see him walking back over a pile of money when he comes to a room with several of them huddled together. The money symbolizes the value of money is nothing in this new society as the only resource that is worth anything is life itself. It also has a bigger symbol for the whole of the film in that the expiremental drug was released far too soon in order to meet market demand and thus the motivation that got it into people's hands was profit, and that has been utterly destroyed.
Mannequins
Robert has set up multiple mannequins at a dvd rental shop. They are a symbol of Robert's isolation and need for human connection as he makes it a daily routine to see them and interact with them. He's given them names and personalities and they've all become real to him in a world where he is completely separated from human contact.
Lion in the Street
At the opening of the film we see Robert hunting deer which he stops going after when he sees a lion kill one. This all happens in Times Square. It is a metaphor for the earth and humanity becoming wild and returning to nature once again. Nature has overtaken mankind and its capacity for growth.
Routine
Everyday Robert has a routine that he strictly abides by. He works out, traverses the city for supplies, watches old tapes of television and runs experiments. His routine is his disciplined nature from the military overtaking his collapsed emotional state of lonliness and isolation. It is a symbol that he is willing himself to carry on until he finds the cure for the virus.
Butterfly
Robert sees a butterfly tattoo on Anna as one of the infected is breaking down the glass that is keeping them from being killed by the mob in front of them. The butterfly is a symbol for Robert's past, present, and future all colliding. It is a divine moment in which his purpose and destiny are clear. His daughter's voice clicks into his head telling him to look at a butterfly once he sees her tatoo right in from of him, and once these two things connect he knows that he must protect Anna so that she can carry on the mission of giving the antivirus to the rest of the world, thus saving the human race.
