It's not even a fair competition to include Wii Sports; as a bundled game in roughly 90% of the gaming world, it's going to sell better than anything in the history of history itself (or the history of this generation, whichever comes first). Wii Fit and Wii Play both have similar potential for insane sales, due to being bundled with peripherals that are so useful.
So, excluding those obvious ones, I'd say... Nintendogs. It's officially surpassed the previous holder of the "highest non-bundled sales count" title, Super Mario Brothers 3. I doubt much is going to threaten to unseat it from that position that's also not bundled.