Well, I used to have one username /password per site and as you said it does get to be a bit much after your 100th site..
Basically what I did was consolidate my sites using HostGator webhosting for the small sites. Get the swap package I think it is, and you can host unlimited websites. I have 3 swamp hosting packages with them and host about 20 sites per package. I log in using one FTP and the sites are divided by folders. It makes it easy to manage multiple sites.
I also use Excel and lots of notepads with specific site information like database information.
I'm somewhat unorganized right now, I need to update a lot of stuff but I've been busy doing other things.
It's not that hard though, find a webhost that you can use for multiple websites and it'll make things easier. I did a lot of research and found that Hostgator (which is hosted at The Planet) is the most reliable webhost out there.
Good luck!
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