Tracking which job you applied for is the least of the job applicant's concerns when looking for a job. In some circumstances the first step of the job application process is even fire-and-forget, and tracking those only serves to not apply again which is a zero-effort move.

Once you start to get a process going, emails and calendars already leave a good, easy to follow paper trail, and any need you might have is easily fixed with a text file/spreadsheet.

For me, I just have a big plain text file where I keep notes and stuff about companies once they get back to me after I send off a resume. I also have two email folders (one of all job search related stuff, the other for messages about upcoming or pending calls) and iCal.