Other than version exclusive Pokemon, which one of Ho-oh or Lugia is encountered first, and which Lati is event exclusive. I'm having trouble deciding which version to buy.
Vulpix, Ninetales, Meowth, Persian, Ledyba, Ledian, Teddiurs, Ursaring, Delibird, Skarmory, Mawile, Gulpin, Swalot, Groudon, and Lugia are exclusive to Soulsilver while Mankey, Primeape, Growlithe, Arcanine, Spinarak, Aridos, Gligar, Mantine, Phanphy, Donphna, Sableye, Baltoy, Claydol, Kyogre, Mantyke, Gliscor, and Ho-oh are exclusive to Heartgold
In Heartgold, you fight Ho-oh when it's at level 40 and Lugia when it's at level 70, and in Soulsilver, you fight Ho-oh at level 70 and Lugia at level 40.
In Heartgold, you get Latias, and in Soulsilver, you get Latios. (Unless you got the event.)
In the main story in Heartgold, you go to Bell Tower first, in Soulsilver, you go to Whirl Islands first.
Those are the only ones I could find, so comment if I've missed any!