It can be done using symbolic links, but these do produce further problems (see below). My setup is currently as follows:
120GB SSD (SSDa)- Windows OS & 64bit apps
60GB SSD (SSDb) - 32bit apps
1TB HDD (HDDa) - User profiles & documents
750GB HDD (HDDb) - Backup (disk images), Fraps & Photoshop cache
--------------------------
It took some time to get it right, but basically I did was the following:
- Complete a full Windows installation on SSDa, boot into windows and assign your drive letters as you would prefer (like my SSDa is C:\, SSDb is A:\, HDDa is U:\, HDDb is B:\, F:\ & P:\).
- Then using the Win7 recovery console (boot-up using the installion media and find it in the repair options) you'll need to reassign all the drive letters to match those used in Win7 earlier.
- While still in the the Repair Console, use XCOPY to make an exact copy of "C:\Program Files (x86)" & "C:\Program Files" on your HDD (this can be with any folder structure, such as B:\Progs & B:\Progs32) to make life quicker

Code:
xcopy "C:\Program Files" B:\Progs /q /e /k /r /h /x /y
- Next, delete the above two C:\ directories completely, including their folders (you may need to change your permissions to do this).
Code:
takeown /f "C:\Program Files (x86)" /r /d n
icacls "C:\Program Files (x86)" /grant administrators:F /t
- Finally, create symbolic links for each folder, using the mklink command (eg mklink /D "C:\Program Files" "B:\Progs").
Boot up Windows
. If all has worked correctly, every time you or a program tries to access "C:\Program Files" it will be redirected to "B:\Progs". I'm on my work PC at the moment, but if I remember correctly you'll even be shown to be in your C:\ even though everything is in your B:\
.
--------------------------
I nearly thought I'd lost the links I've used in the past to help, but found them on my mobile (still accessible without my PC booting
). The most helpful site I found was this one: VistaHeads. There was a second site, but everything you need form it is in step 4.
--------------------------
The biggest problems I've had are with Windows Update & Adobe installations where the updates/installation routines are hard coded to use C:\xxx which does not recognise that you have the symbolic link in place. The work around... edit your registry to replace "C:\Program Files" with "B:\Progs" and all should work perfectly after that. With Adobe's installations, attempt the installation and allow it to fail, then edit the registy as the entries are then created for you by the failed installation.
Past experience (I've done this about 4 times now thanks to not knowing the above and a HDD failing on Night 1, before backing up) has made me realise just how important step 2 is. You can skip it, but you can have other problems. When loading up your Repair Console, you might find that your C:\ is now X:\ and B:\ is now C:\. While this is fine for XCOPY, the symbolic link creates problems:
If you then try to create your symbolic link, it's possible it won't work at all. If you were to use the mklink example above but this would actually place it in your B:\, then when you load Windows, it will recognise your C:\ correctly but the physical link will still be in the B:\ causing all sorts of problems. So, what if you were to try: mklink /d "X:\Program Files" "B:\Progs", yes it will place the link in the Windows C:\, but when you load windows the link will be in a non-existant X:\. So, in both examples your Program Files will be unavailable. I found this out with my User profiles being missing and causing all sorts of login issues
Bookmarks