The best replacement for popup is pop-up.

The best alternatives to popup are rated as following:
★★★★★  pop-up
★★★★★  modal
★★★★★  new window
★★★★  popup
★★★★  popover
★★★★  tent
★★★  travel trailer
★★★  modal window
★★★  lightbox
★★  dialog
★★  popin
★★  handcent
★★  iframe
★  overlay
★  teardrop
★  pop up
  adorner
  popunder

Your alternative for popup is not listed? Suggest!
Speaking about popup, one probably shouldn't forget about fancybox.

Other search terms related to popup and their ratings are:
★★★★★ fancybox
★ window open
You have in mind a companion for popup and it is not yet here? Propose!



Google Trends

Scale is based on the average worldwide traffic of popup in all years. Click on graph for more.
popup
pop-up
modal