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.

I believe you can run the old Shadow Warrior and Duke on Vista 64 but you would need to know how to set up DOSBox in order to do so. Not knowing your skill level with DOSBox makes it hard to give recommendations on setting it up and patching the games on Vista 64. You need to understand how to extract 16 bit patches, move files to the correct folder and possibly update any file paths/ file names in the game ini, win.ini and sys.ini (if the games write info there) and set up the config file for DOSBox. Covering all of these problems on a forum thread would be difficult at the least and one problem leads to another.
As in my first post I make the following suggestions . . . if you don't want to master DOSBox :
One way to run Duke is using the eduke32 port. How to install here.
One way to run a Shadow Warrior game is using the JonoF's Shadow Warrior Port (JFSW) , a native windows port, How to install here.
These are both windows ports so it may be more work than you want but it brings you out of DOSBox. You need some of the original files for both games using the ports. I run the Duke port on my Vista laptop with no problems, don't have Shadow Warrior so I can't comment on the port stability. Eduke32 was easy to setup.
It is not the solution(s) you are looking for but you may have a better chance of getting both games running with the above ports or . . . do some research on DOSBox configuration and set the games up using DOSBox . . . worrying about patches and mods after you get the games running.
Hope this helps . . . . =)
Edit: DosFreak has some very good input as well, get the Universal Extractor here or 7-zip here or VMware Player here.
Gotta ask, same Dosfreak as the DosFreak posting on vogons.zetafleet.com or compatdb.org or etc, etc ?? If so, if you can't help I certainly can not . . .=)

The games where already changed (using dosbox somehow) to make the games work, so mabey I can figure out dosbox. Thanks for the help.