Diamond, it's my empoleon and luxray (as the 'bosses') Strongest? I dont know. My gyarados or gaburaisu? Dunno. All have their strengths.
Pearl... the Boss is the level 24 bibarel, because she's the only sensible one when compared to the infernape, golduck and crobat. The same pokemon that beat the league whilst toting moves like scratch, atsonish (AND bite. In one moveset), confusion, flame wheel and water pulse. Because she's more awesome than Arceus.
Platinum is probably the gyarados, but they're all... well, no, my drapion is also on a 'boss' status. The strongest? I don't know.
HG's Boss is the feraligatr. Mostly because the only ones that can be bothered arguing are the metagross (who is just a smartass who's all sass at him) and growlithe (who's only after a fight, not for any greater reason). Strongest are my metagross and feraligatr, but it's mostly because I haven't let my pidgey, larvitar, growlithe or togetic evolve yet (but level 49 is so close. SO CLOSE!)(but I don't know why I haven't evolved my growlithe.)
SS... there is no boss. Unless it's my typhlosion. But on a team of two (and two HM masters) there isn't much to say about the matter.
And I just went on for far too long t`_t;