I'm a computer programmer (by day--writer by night :D), so I wrote a program to keep track of my submissions. With it, I can enter information about the stories I have written (title, genre, word count, type--short story, novel, etc.); markets I want to query (magazine/publisher's name, type of medium--e-zine, print mag, both, etc., genres they accept, turn around time, etc.); and then, I put these together to create submission records for each location I send a story. When I receive a response, I can update that particular submission record by filling in what the response was (form rejection, personal rejection--in addition to the message the editor jotted, etc.) and the program will apply date formats for me to show what the actual response time was. All of these records are presented to me in a historical report format so I can open any prior submission to see where the story was submitted previously and what the status was, if that information exists. There's more functionality to the application, like showing a list off all of the stories I've entered and what their status is (never submitted, pending response, accepted, etc.) that can be filtered to show me certain criteria I want to know about a given story.
Before I ever submitted my first story, I heard other writers discussing keeping their submissions organized, so I decided to write this custom application for myself to help me with organization. While writing it, and submitting, I tweaked the program to provide more functionality as it became desirable. I've given a copy to one of my writer friends and he seems to enjoy using. I've been thinking about adding it to my website as a free download for any other writers who might like to use it (free of charge and for use as-is). My only concern, however, is that people will want to contact me requesting additional functionality or to provide bug reports. I want to spend my personal time writing stories and not computer code. Therefore, I haven't made it available to the general public. If anyone wants to play with a copy to see if it might help them keep track of their submissions, you can email me and I will send you one.