If you're still around, please try installing it in a Windows 2000 bottle. After it's installed, open the bottle manager, select the bottle you installed it to, go to Control Panel -> Wine Configuration -> Graphics, and check "Emulate a virtual desktop". With these settings SimCity 3000 Unlimited Edition works perfectly for me on Linux. I think it will also work with other SimCity 3000 editions and on OS X, but I have no way to test this.
I made a CrossTie to automate these tweaks. Once it's approved by the CodeWeavers ninjas, SimCity 3000 should "just work" in CrossOver without having to make these changes manually.