OK, here are a few more things I find myself missing:
The chatroom window should have a menubar.
Chatroom roster entries should have more stuff on their context menus, for instance “View Profile”.
The chatroom window should remember the relative sizes of the panels, not just the window size.
Fonts should be settable.
A disco browser would be nice…
The shortcuts on OS X are incomplete/bad/missing.
There should be a command + w to close single windows (read: alt + f4 for windows).
Popups should not be modal. When editing prefs and engaged in IM or Conf. I cannot do both. Doesnt make sense.
Totally agree on the modal dialog(s). I don’'t know why I even did. We are actually working on some new notification systems that will not use popups but rather more elegant ways of notifying users of subscriptions, conference invitations, etc. You can track this issue schedule for the 2.0 release with SPARK-330.