Putty is a program that runs on Windows which allows remote access to other machines using the SSH protocol. Once you gain access to the remote machine which must be running an SSH server (unless you are using port-forwarding), you are presented with a console as in Telnet. The difference however, is that the connection is secure. From that point on, you can run any programs you would normally be able to run at the console.
I mentioned port forwarding earlier, and this is one of the popular uses of Putty. It can be used to create a secure channel between two machines, through which any TCP protocol can be tunnelled. Thus you could run POP3, RDP, VNC or any such protocols/applications securely over the internet between any two hosts.
If you let us know what you plan to use Putty for, we should be able to be a bit more specific or at least point you in the right direction.