Just came here to say that I have struggled with this in the past too. I used plain text for tracking, and reduced the number of parallel application to something managable as a workaround. I would have loved a sort of CRM that not only keeps track of application and interviews, but also store my homework and personal notes for the interview and similar resources.

EDIT: I also create slightly customized resumes for each type of job I apply to. (E. g. backend, system development.) To keep track of which resume I sent to a particular company, I just keep multiple PDF. The process is tedious, especially when I need to update something in the base resume, like adding an experience or a technology.