Just had this happen to me today. I went to a website (not sure which exactly): got a MacKeeper 05 popup window. Quit Safari. Re-opened Safari, and the first screen to appear is the MacKeeper 05 window. Went to Sarfari --> Reset Safari. Quit and re-opened Safar, and the problem is fixed.
I'm not exactly sure what they are doing, but it is obvious that they are exploiting some kind of security flaw in Safari. Something is allowing them to do a persistent popup that is retained after a reboot of the computer. I agree with previous posters that this software is adware at least, and may contain some form of spyware. Thankfully it is not a real virus, as it does not get into the system files (Previous posts about removing zeobit files are only accurate if you had the misfortune of actually purchasing and installing this software). In my case: root# find / -name *zeobit* returned no results.
If you just got this pop-up through an advertisement, reseting safari will fix the issue. FWIW, I'm going to send a note to our Apple Reseller to let them know about the issue.