There is an extremely unreliable method which I never tried:
Microsoft does not support changing the location of the Program Files folder by modifying the ProgramFilesDir registry value
I've seen stories of people modifying the registry to change their default directories around, but keep in mind that any badly-programmed application (i.e. they hard-coded "Program Files") will crash.
That said, I'm using 48.6 GB on my SSD (partitioned 80 GB of it) and I installed Windows 7 and everything EXCEPT games on it. (including larger programs like Microsoft Office 2010, LibreOffice 3.4, and Eclipse IDE) There's no reason you need to put every single application on the hard drive unless you have one of the old stuttering SSDs.
As for your downloads folder, I use this method to put it on my hard drive:
Redirect a folder to a new location
It works with every folder with a special icon in your Users\<your user name>, but for some reason some programs get cranky if you move "Favorites" and "Links".