I believe I know the answer but I wanted someone who is better versed in SP2010
and upgrades to confirm.

It appears that custom apps for SP2007 that were coded to use
Microsoft.SharePoint.Portal.SingleSignon (SSO) will not work after an inplace
upgrade. Is this correct? Do we need to recompile our apps to use the new Secure
Store Service (SSS) or should our apps still retain backwards compatibility? I
can't find any docs that specifically say what needs to happen.

I'd be fine if we'd eventually have to reference the new assemblies and
recompile but to be required to recompile apps and upgrade the solution right
after the farm is upgraded seems more than a bit annoying.