If your machine won't boot when you remove what should be a non-boot disk then there must be something at the OS level configured to look to that disk. The only things that comes to mind at that level that you can move off the OS disk is (a) page file and (b) user folders i.e My Documents. I wouldn't have expected either of those not being found would cause such a catastrophic failure but you never know and it's worth ruling out.
You don't mention which version of Windows you're running but there's instructions here for XP on how to move the page file to a different partition here so just look at that:
http://support.microsoft.com/kb/307886Moving My Documents is done like this so have a read of that:
http://support.microsoft.com/kb/310147I'd also go into the BIOS and check the various settings in there and just make sure nothing is pointing to or expecting the secondary disk to be present.