I think cover letters are very valuable. You are drawing attention to the points in your CV that the employer wants to see.

Reason you can't store them the same as a CV is that they are supposed to be taylored to the job you are applying for.

ETA - when I was going through resumes, the ones that didn't have a cover letter showing the specific experience I was after didn't get a look in, unless I didn't have enough candidates, or was feeling generous. If you can't answer what I want in a cover letter, it makes me think you aren't really that interested in doing what I require for the job.
This is pretty much exactly what i was going to say. When i get a cover letter i see it as the person has taken the time to put effort into applying for the position. It makes it easier to see what parts of a resume are relevant to the position with out having to read every part of the resume (i have never understood the interests section. I personally don't care what a persons outside interests are if they have nothing to do with the position!) You can still make a cover letter sort of generic, especially if you are applying for similar jobs. Just make sure its edited accordingly and double check to make sure you don't leave any info from a previous job in there!