Speaking in a showreel unveiled on stage as part of Nintendo's E3 press conference, Hideo Kojima confirmed that he is experimenting with how Metal Gear solid will work as a 3D handheld title.
Before Kojima's comment was screened, Nintendo president Satoru Iwata unveiled a list of publishers supporting the 3DS during the conference.
These include: Activision, Atlus, AQ, Namco Bandai Games, Capcom, EA, Harmonix, Hudson, Konami, Tecmo Koei, Level 5, Majesco, MMV, Rocket, Square Enix, Sega, Takara Tomy, Take-Two, THQ, Ubisoft and Warner Bros.
Iwata specifically name checked new 3DS games spun off from big franchises including Professor Layton, Batman, Metal Gear Solid, DJ Hero, Madden, Saints Row, Assassin's Creed, Kingdom Hearts.
Then Kojima stated "I'm experimenting with what Metal Gear Solid would look like on a 3D handheld display," suggesting that the title may be in a very ealry stage of its development.
UPDATE: The 3DS Metal Gear Solid game has been named in a Nintendo press release as MGS Snake Eater 3D 'The Naked Sample'.