I've changed it up many times since HGSS was announced back in September '09, but:
-Totodile
-Shiny Pichu
-Shaymin
-Gastly
-Arcanine
-Lugia
I've finally decided on my starter (as I wrote this, lol!). The decision was a result of elimination, actually: I'm using Shaymin as my grass type, so I don't need Chikorita, and I'd rather use Arcanine who now has Morning Sun as my fire type. Finally, there's no other water type I care to train until waaaay later when I can catch Suicune. I love them all equally, but Totodile fits best.
I'll evolve the Shiny Pichu into Pikachu as soon as I'm sure it won't void the Spikey-Eared Pichu event, though I'm almost certain it would still work. I'll never evolve it into Raichu.
Since Shaymin is restricted from Battle Tower, in-game is the only time Shaymin gets to battle, discounting competitive battling, of course. Plus, it's just awesome!
I'll catch that Gastly as soon as the sun sets. Gengar is one of my fav pokemon. Duh, my username?
The aforementioned Arcanine serves as my check against Pryce and Jasmine.
Lugia will be a permanent member of my team. It's arguably my fav pokemon, and it has been AGES since I had one (like, the original G/S).
When I reach Kanto, I'll have many options (too many, actually). Suicune, Zapdos, Latios/Latias, Groudon, Kyogre, Rayquaza, Mewtwo, and Ho-oh are all possibilities.