I use Excel. I highlight the name when I add a submission entry and remove the highlight if I get a rejection. I change the color for a request. Makes it easy for me to see the responses I'm still waiting for. I also include what was sent, email or snail, when, the agency, date of response, and finally, any relevant notes I have or comments received. At the bottom, sometimes I list names I still plan to send to.
It works pretty well for me, anyway. I like having it all in one place, easy to see and ctrl-F searchable.
For that reason, I personally wouldn't bother with other software or websites. I know some people use querytracker, though.