
The overall list of newly incompatible programs is actually pretty small and heavy on security applications. You can get the full list of apps that won't work with Vista SP1 at Microsoft's support page here.
I've never even heard of most of the other apps on the list (Fujitsu's Shock Sensor, part of its laptop add-on software, and the New York Times Reader software are the exceptions), so most people won't experience issues. The most common apps, the three mentioned in the first paragraph above, simply won't load after you install SP1, so there's no additional risk of your PC crashing or you losing data... but you might find yourself suddenly without virus protection, so be warned.
There's unfortunately nothing you can do about these program incompatibilities except to wait for the vendor to fix the problem or install an alternative solution. In most cases, I expect those fixes to be available within the next few weeks, hopefully before SP1 actually ships, but some may very well linger.
Also note that this list reflects only software that is newly incompatible with Vista. There are no up-to-date incompatibility lists available on the web (most date back to last summer or earlier), and Microsoft has never provided one itself. That's a long way of saying that if you have an app that doesn't work with Vista now, it isn't going to suddenly start working when SP1 arrives. (Try Compatibility Mode!)
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