You're not the only one... and I manage them by naming my download folders by month and yeah, example:

Oct-Nov2012... this way I can keep track by how long ago I may or may not have downloaded it. It helps me a lot...

As for organizing runtimes, I have 4 runtimes... one for Poser 7 which only has the content it came with, one for Poser 9 which also only has what it came with... Then one on my first external harddrive called !X!Poser7 which was stuff mainly for older versions... Then when I got Poser 9 I bought a new external harddrive and made another runtime called !X!Poser9 which contains P9 compatible content...

Although I'm sure there are other better methods than mine, but these work for me.