I can confirm that a lot of those games work perfectly fine under modern machines and operating systems, and are actually better in many cases since you can get custom widescreen resolutions and full antialiasing/anisotropic filtering.
Unreal and Unreal Tournament play great on modern machines. You can get today's resolutions and proper widescreen FOVs with some quick edits. As I'm sure many here already know, www.wsgf.org
is the place to go for that info. The site also has a nifty patch for SiN that edits resolution hex values for you. Check the Steam forums for a replacement DLL file if you get a buffer overrun error upon SiN's startup.
You don't have to worry about a game like Tomb Raider or Unreal running too fast if you simply enable vsync.
For games that run under the Glide renderer, a quick install of nGlide
will give you a top quality Glide solution that supports modern resolutions. This is especially useful for a game like the original Tomb Raider. Some other games that use Glide natively support Direct3D or OpenGL as well, so a Glide solution isn't needed in those cases.
Then there are of course OpenGL source ports for games like Quake and Quake II that provide effects and resolutions well beyond what a retro system will allow. I recommend "DarkPlaces" for Quake, "KMQuake II" for Quake II and "GZDoom" for all of the DOS-based Doom games.
With Creative ALchemy you can even re-enable EAX effects in older games if you have an X-Fi sound card. For a top quality MIDI solution, I recommend the SGM-V2.01 SoundFont for use with an X-Fi card. MIDI-based games like Sam & Max and the Doom series sound great with it.