ComicBook (via ComicBookMovie). They have dug up information that "could" point to Namor the Sub-Mariner being involved in Iron Man 3. That tidbit includes a special effects water tank. Previously there have been rumors of Madame Masque and Ghost being the villains of the third installment.
"We’ve also been snooping around for any info on potential villains for Iron Man 3, but no one seems to have any official word yet. However, some things we have uncovered about the shooting location and the choice of production facility does lend itself to some rather interesting Iron Man 3 villain speculation."
"While tax credits played a role in the choice of the coastal town of Wilmington, North Carolina as a filming location for Iron Man 3, the production facilities at EUE/Screen Gems Studios were also a factor. EUE/Screen Gems Studios has a 37,500 square foot sound stage that includes a special effects water tank."
Currently the only confirmed players include Tony Stark/Iron Man (Downey), Pepper (Paltrow) and Rhodey/War Machine (Cheadle). Marvel has stated that this film won't include Avengers cameos. I'm not sure if that includes SHIELD agents but don't expect Cap, Thor and Hulk showing up. The Iron Man franchise has a history of introducing new Marvel universe characters so I wouldn't be shocked if this ends up true.