First we need to "backup" the data from our "Program Files" folders. We can use xcopy to do this:
It will ask you if "Program Files" is a file or a directory. Press 'D' to select directory.
xcopy /S /H "C:\Program Files" "E:\Program Files"
If you have a 64-bit system, then do the same thing for "Program Files (x86)".
Now all we need to do is set up hard links on the folders in "Program Files" to point to the folder on the HDD instead. You can pick what programs you want to do this to. I leave my games on the SSD (because I like the performance), and other programs like Skype get moved to the HDD.
To link a folder all you have to do is delete the current one (be certain you've backed it up properly!) and create a hard link with the same name:
rmdir /S /Q "C:\Program Files\Adobe"
mklink /J "C:\Program Files\Adobe" "E:\Program Files\Adobe"
Related reading: LifeHacker - Move the Users Dir in Win 7
Other copy options include windows robocopy:
or a Linux Live CD:
robocopy /S /Z /R:0 /W:2 /V /MT:4 "D:\Program Files" "E:\Program Files"
cp -ar <source> <dest>