I have developed a sort of system while doing the job hunt. It's always being improved and it saves me many headaches. Maybe I'm obsessive about it, and maybe I'm crazy. But it works for me and that's all that matters.
1. I save every resume I submit in a separate folder ordered by company name.
2. I save every cover letter I submit in the same way I do resumes. In other words, I have a TON of resumes and cover letters.
3. I have a general resume and cover letter I can print out at a moments notice in case I meet someone who might know of a job opening.
4. I keep plain texts versions of my general resume and cover letter as well for the same reason. Some companies only accept plain text for some reason.
5. I have a references document listing the contact information of all of my managers, bosses, and important people who I trust to vouch for my experience.
6. I keep track of which jobs I've applied to, and which interviews I have gotten.
7. I have details of a bunch of companies in the Orange County area, along with websites, contact info, account info I use to login to their sites, and many other things that would fill up 10 posts.
It may all not be necessary, but so far I think it's working.