I was able to successfully install DS9: The Fallen in a Win98 bottle on the following machine:
Soyo SY-7ISA+ Intel i815 Motherboard
Intel Pentium III 866 MHz Processor
512 MB SDRAM
PNY Verto GeForce FX 5200 AGP 8x 256 MB DDR
Creative Labs Sound Blaster Live! 5.1 PCI Sound Card (SB0220)
Samsung CD-RW/DVD Drive Model: TS-H492A/RSWN
Dual Boot openSUSE Linux 10.3/Windows XP Pro SP3
CodeWeavers CrossOver Games for Linux Version 7.1.2
I used the autorun method to install the game with no difficulties.
I played part of the way through the Sisko training mission, and I haven't noticed anything that doesn't work. I did have to use a 1024x768 virtual desktop, and even then the game insists on playing in a window. I also had to create a Hide button on the Linux toolbar at the bottom of the screen and make sure it slides out of the way before starting the game so I can see the entire window. Both the software and OpenGL renderers work, and the game works at all of the resolutions I tried to use. Performance seems to be quite good.
I had no problem applying the retail patch (Patch112100-a.zip) and the English Mini Code Patch (DS9 The Fallen - Exe and Joystick Patch.exe).