When I moved my boot drive over to a 64GB SSD, I knew I was going to have to keep most of the larger files on my mechanical drive, but I didn't really want to have some applications running from C:\Program Files and others running from E:\Program Files. I wanted to keep my new SSD setup as close to my previous mechanical primary drive setup.
My initial reaction was to try to mount the mechanical drive as a folder within the SSD drive, but this was rather limited. It may as well have just been a different partition rather than a partition inside another partition.
The solution was to use NTFS Junction Points. They are essentially the same as symlinks in the Unix world. These are essentially shortcuts from one folder to another, but applications cannot tell the difference and treat them as the same. This means I can move my Downloads folder to my mechanical drive, create a Junction Point from C:\Users\username\Downloads to E:\Downloads.
Clicking into C:\Users\username\Downloads shows the contents of the E:\Downloads folder, and no changes are required in any applications.
To create a Junction Point, first move the folder location using the Location tab in folder Properties (only required if the folder is a special folder such as My Music, My Downloads etc.), delete the original folder, and then create the junction point using the mklink command from the command prompt. Your command prompt will require administrator privileges to do this.
C:\Windows\system32>mklink /J C:\Users\username\Music G:\Music