It seems that Transformers: Dark of the Moon may return to theatres or at least to IMAX again according to a post in the Shoot for the Edit forums by Michael Bay. He wrote, "I think they are really considering re-releasing Transformers on IMAX again. From what I heard from Paramount."
I am not exactly sure when Paramount would squeeze into the IMAX schedule as the year seems locked up with Contagion (released date 9/9), Real Steel (10/7), Puss in Boots (11/4), Happy Feet Two (11/18), and Mission Impossible 4 (12/21) on the schedule. Often the studios will have contractually set date run for their IMAX releases in part to lock out the competition and also because the conversion to IMAX format has its own cost they want to make sure to recoup. A return to IMAX theatres might just be enough to overcome the $23.6 million deficit (likely around $10 million by time international run finishes) to become 4th on the all-time box office list. As of now it does seem to be a long shot.