Mine is a simple table that looks something like this:
Manuscripts 2009 (this is the heading)Title..........................Publisher.......Date Sent.........Reply............CommentsGrace's Big Chase Henry Holt 10-18-08 Rejected Responds if interested
That is a sample entry. In the past, I have included a column for "publication date" and "payment," mainly for magazine pieces. I'll probably add those in if I ever get around to submitting to magazines again. Make sure you keep a back-up file of this spreadsheet in case of unforeseen computer trouble (gasp!).
Other fairly simple methods of keeping track of your manuscript submissions is to keep an actual file folder with manuscript tracking forms in it--one sheet per story. Put the title at the top and then make columns for publisher, date, reply, comments, etc. Of course, this is a little more tedious and harder to search. Then again, if you do it that way you won't lose it if your computer crashes. You could also do the same thing with index cards and keep them in a recipe box. Sort them by genre/format/age range if you're a really versatile writer like me (grin).
Whatever your method, keep it as up-to-date as possible.