I've been stumbling upon this bug for a while now, and keep having to remember how to fix it. Tired of googling it every time (and it's never in the top results), I thought I'd write a short entry on how to enable line numbers when there doesn't seem to be an option for it in CFEclipse 18.104.22.168.
There's actually a bug filed over at the CFElipse tracker, so I'm guessing this will be resolved in the next release. In the meantime, here is the fix I found towards the middle of this Google Groups discussion.
Navigate to your Eclipse workspace on your file system. From there, open .metadata, .plugins, .org.eclipse.core.runtime and .settings. Edit the org.cfeclipse.cfml.prefs with notepad and add this line:
Close the file and restart Eclipse. Your line numbers should now show in your gutter. Enjoy!