I think the easiest way to explain it is this: First, you want to start with making certain that your hardware accelleration works with X Windows. The easiest way to do this, is to open up a terminal window, and enter
glxinfo | grep direct
if this returns 'direct rendering: Yes', then you are in good shape. If it returns 'direct rendering: No', then you will need to diagnose why this is. Likely with ubuntu, using the hardware you've listed, you'll just need to install the nvidia drivers from the Non-Free repository. Once it's installed, and you've restarted your X Windows server, try that command again. You're looking to see that you have direct rendering.
Once that's in place, you will want to install WINE. Again the usual package installation tools for ubuntu should be of assistance there. once this is done, open a terminal, and run
winecfg
In the resultant window, make certain to click on 'drives' and confirm that the settings for your CD/DVD-ROM drive are correct. (Often times, clicking 'auto detect' will set up things just fine) Click Apply, then close this.
Next, install Prophecy, and either the Secret Ops starter pack, or Secret Ops from its Prophecy Gold CD. To do this, place the CD in the drive, mount it, and then from a terminal enter in:
cd ~
wine /path/to/cdrom/SETUP.EXE (or setup.exe, Setup.exe, whatever the actual capitalization is. I don't have my CDs on hand at current)
Install the games with whatever options you wish. When prompted to swap CDs, be certain to drop to a terminal, and
umount /path/to/cdrom
then eject the cd, place the requested one in the drive, then mount the new one in the same mountpoint.
Once Prophecy and the Secret Ops are installed, install Pedro's OpenGL renderer for the games you have installed. (The link can be found around the CIC, I'll add it here later.) run
wine OGLsetup.exe
from both your Prophecy and Secret Ops directories and set up your desired resolution and such.
Follow this with
wine launcher.exe
From there, in video options, select the OpenGL renderer, then launch the game. That should do it. If you wish to install Standoff, just run the installer that you've downloaded. Standoff comes with the OpenGL renderer already. Unknown Enemy can be a little trickier. I posted earlier in this thread the trick to getting the OpenGL renderer to work with it.
That SHOULD be all that really needs to be said about running the Vision Engine games under WINE.