While working on a Drupal project this week which used popup windows to create nodes that were linked via node reference fields, I started running into major stability problems between a variety of modules that were being used, particularly Popups_Reference and Vertical_Tabs. Popups_Reference is a pretty neat little module that uses the Popups API module to provide the interface and lets you add buttons underneath a modal, which Vertical Tabs is a new interface style used heavily in Drupal 7 which presents form framesets as a series of vertically-aligned tabs; this module is a port of the D7 code for Drupal 6.
I happened to tweet about fixing Popups_Reference and had several people reply that Popups API had been deprecated in favor of Modal Frame API (Bangpound) and I should try using NodeRelationships instead (JerDavis, Hefoxed). Looking at the Popups API project page it actually says:
This module is not currently maintained. Please check out http://drupal.org/project/modalframe, or contact me if you would like to become a maintainer.
While the project could be continued, with ModalFrame having lots of support from other modules and being a core part of Drupal 7, it makes sense to just deprecate Popups API entirely and move all modules to using ModalFrame instead.
Towards the goal of deprecating Popups API I have added / updated tickets for a number of modules to promote this effort:
In the interest to helping to organize the effort I've added an issue tag "Popups API deprecated" which can be used to quickly see which modules have been migrated or deprecated.
If you use one of the modules above I strongly urge you to get involved and help the effort to migrate it to using ModalFrame.