According to some posts on Hideo Kojima’s English twitter account, the Metal Gear Solid HD Collection will include the versions of Metal Gear 1 and Metal Gear 2: Solid Snake that were in Metal Gear Solid 3: Subsistence, as that is the version of MGS3 that they’re using for the collection. There is no word on if it will come with Subsistence‘s version of Metal Gear Online or Existence, the cut-scene re-workings that were part of Subsistence‘s limited edition. They will also be using the Subsistence version of Metal Gear Solid 2.
There are a few differences between the western and Japanese versions of the game as well; the Japanese version will include a product code for Metal Gear Solid 1 instead of Peace Walker, while we get Peace Walker and no download code. I’m assuming the “product code” is so you can download the game off of PSN, since it’s been released there. I’m not sure if they’ll be doing the same thing for the 360 version of the game in Japan. (They probably won’t, if they’re even releasing the 360 version over there.)