Below is a patch to FileDataObjectManager in the latest SVN of DOM to allow Uploadify fields to respect uploadFolder & allowed extensions. UC: is there an issue tracker / other workflow that's preferred for patch submissions?

Index: www/dataobject_manager/code/FileDataObjectManager.php
===================================================================
--- www/dataobject_manager/code/FileDataObjectManager.php (revision 14)
+++ www/dataobject_manager/code/FileDataObjectManager.php (working copy)
@@ -293,6 +293,16 @@
}
}

+ // [start] bb patch
+ if(!empty($this->allowedFileTypes))
+ {
+
+ $uploader->setFileTypes($this->getAllowedFileTypes(), $this->PluralTitle() . '(' . implode(',',$this->allowedFileTypes) . ')');
+ }
+
+ $uploader->uploadFolder = $this->uploadFolder;
+ // [end] bb patch
+
return $fields;
}