According to this post on Daring Fireball a new iPhone SDK Agreement release in conjunction with the iPhone OS 4.0 announcement today specifically bans any iPhone appli
This has been causing friction between apple and developers since they first opened up cocoa touch.
There was the Commodore 64 issue: http://gizmodo.com/5354422/commodore-64-iphone-app-approved-removed
The c-64 emulator allowed access to the basic CLI and was removed by apple.
There was also a lot of discussion on the Lua list: http://lua-users.org/lists/lua-l/2009-10/msg00015.html
Lua can be built on the iPhone arm processor from the c source so is this considered c or Lua?
Some applications using Lua have been accepted: http://tuomaspelkonen.com/2010/03/why-lua-truly-rocks/
Unity uses scripting languages as a part of its API and many Unity games have been accepted: http://unity3d.com/gallery/game-list/
...including Zombieville which "was recognized in Apple's iTunes Rewind 2009 as one of the top-selling games of the year".
I can't see them removing all of these games at this point.
What people have been most frustrated with is that there does not seem to be a single standard for what is accepted and what is not. Do big players like Adobe and Unity get special privileges to use scripting which smaller groups do not?