How can I patch older games like Duke Nukem 3d and Shadow Warrior. For Shadow Warrior I have a 3d fx patch and a extra levels add on, but when I go to open them Vista says it can't because they are not compatible.
I got both games directly from 3d realms website and now all the forums are closed on there so I thought I would ask here. 3d realms fixed all of their games to work on vista but Im not sure how to patch them.
Any help on patching DOS games running on 64bit Vista would be appreciated.

Since thet are 16bit executables made for MS-DOS then they need to be run in MS-DOS or an environment that emulates MS-DOS like DOSBox.
So run the patches in DOSBox (mount the games properly first before running the patches)

Okay so I download dos box, is it easy to use?

Not the same but . . . I like the eduke32 mod for playing the Duke. It runs natively without relying on emulation of any kind.
There is also a high res mod available. Some say it doesn't work with integrated video cards, works well with my ATI card on my laptop.

it depends. If you remember your way around DOS, then its a breeze.
The only difference it mounting. Since it is an emulator, it doesn't your mount entire file system, but instead virtually mounts a directory of your choosing as c:. You can set a directory to be mounted every time in the config file, along with other options , such as the # of CPU cycles to emulate, Sound card, etc.(the defaults work fine for me).
I highly suggest reading the Readme. It has some good tips/info that really help avoid potentially frustrating moments :-)

Seriously, this depends on the game. Some old DOS games had Windows-capable patch executables after some time. Also, many DOS patches aren't executable at all, they just want to be unzipped into the game folder on top of the old files.
Have you tried simply extracting the files into the game folders? (Don't forget to back up!) I find very unlikely that the patches came in the form of DOS executables...
If you're sure they're executables instead of archives to be extracted into the game folders, you might want to right click them, choose "Properties" or similar option, turn on "Run as administrator" and also "Compatibility Mode" (Windows 98 or XP being your best bets of compatibility mode, but it could be anyone.
Finally, my major secret for classic gaming: get patches for every old game on The Patches Scrolls. These pages include patches for Duke Nukem 3D and Shadow Warrior, including 3dfx fixes:
http://dlh.net/cgi-bin/dp.cgi?lang=eng&ref=ps&sys=pc&cap=d
http://dlh.net/cgi-bin/dp.cgi?lang=eng&ref=ps&sys=pc&cap=s
Hopefully you'll be set.

I tried extracting the 3dfx patch into the game folder, but nothing...Is there a certain place? I also I am certain that the extra maps pack for Shadow Warrior is an exe file. It runs setup, but then it says "error running setup exe"

Make sure you are right clicking the setup file and clicking on "Run as administrator" from the resulting dialog

Yes I am running it as administrator.

I already tried extracting them, but even putting them into the folder doesn't yeild results. And I KNOW that the extra maps for shadow warrior is a setup exe. It even starts setting up, but ultimately fails.

Have you got it running in compatibility mode? Not the game, this setup.exe instead, the one you're trying to use.

RafaelLopez has just posted my only other suggestion, try the different compatibility modes for the setup.exe . . . maybe starting with Windows 95.
Edit: Also most of the old programs ran on ini files. You may have to go into the game ini and set the paths for the new files. Vista / XP has a system.ini and a win.ini for running the old 16-bit apps that use to require writing to these two files back in the day which also may require some path updates.

Okay here are two screen shots of what is happening. One is me trying to run the Extra levels(Wanton destruction) and the other is the 3dfx patch. I tried all compatibility modes and administrator stuff.
http://img37.imageshack.us/img37/3483/swprobles.png
http://img69.imageshack.us/img69/3029/swproblem.png