My 10 cents :
 
dislike :
 - new trayicon for an incoming file transfer : don't spam the systray, it is full of icons as it is;
 I saw people having over 10 icons there. They would hardly notice an appearing file transfer icon ;-)
 - popping up dialogs. That steal focus.
 - popping up 10 dialogs for the more or less same content (like 10 incoming files)
 
 
like:
 - reuse existing conversation window:
  - no new icons/dialogs, that could be "lost" etc...
  - if the conversation window has focus, then the notification problem does not exist
  - if the conversation window has no focus, then it should be handled the same way as a new message
     on Windows , that means the windows icon on the task bar will flash and be colored, until the user clicks it,
     no focus stealing, no jump-in-your-face; I repeat: this is already implemented
  - the information can be displayed in the message pane as already proposed, or
  - the information can be displayed in a toolbar/line especially for that(look for GUI design ideas below)
 
Possible file transfer bar look:
User1 is offering file "Vacation.jpg*" [Accept][Deny][Details]
 
* - do not hide parts of the filename ! like the last 4 characters ;-) 
 
The [Details] button could open the file transfer dialog for more options.
 
Regards and keep it simple,
David