It has been confirmed that, after beating the Elite 4, Groudon and Kyogre are available in HG/SS. However, Kyogre is exclusive to HeartGold and Groudon to SoulSilver. However, getting both Groudon and Kyogre onto one cartridge will unlock Rayquaza.
Scan can be found here: http://pokebeach.com/news/0609/kyogre-groudon-rayquaza-in-heartgold-soul-silver.jpg
Cynthia, the Arceus legend and the Sinnoh Dragons
A scan from July's CoroCoro confirms that there is an event related to Arceus in this game. The scan features Cynthia, the D/P/P champion and Arceus standing in a triangle of three symbols thought to symbolize Dialga, Palkia and Giratina.
There is a new map of Johto in the CoroCoro scan: http://img199.imageshack.us/img199/6808/hgssscans1.jpg
There now appears to be a river running alongside Route 45 (Blackthorn to New Bark). The Magnet Train's track (Goldenrod to Saffron) appears to be now visible on the map. A new area has appeared to the West of National Park (The big pokeball)
The map features the small sea section to the east of New Bark town (heading east towards Tohjo Falls) which leads into Kanto. Route 28 (a Kanto route leading to the Indigo Plateau can also be seen). A small section of the Indigo Plateau and Mt. Silver can be seen to the extreme right of the map.
There have been two confirmed changes in the game, the first being the introduction of wind effects in New Bark town. It was also been confirmed all 493 pokemon could follow you in this game.
http://i60.photobucket.com/albums/h5/jippily/HGboxart.png - HeartGold boxart
http://i60.photobucket.com/albums/h5/jippily/SSboxart.png - SoulSilver boxart