Konami does come to mind but I think they are more slow to get on the boat than flat out missing it. Elebits and Dewy were respectable "were not going to put more than one egg in the Nintendo basket after the Gamecube until it proves itself" efforts. MLB Power Pros was a great game that is obviously much bigger in Japan, and they are making a major effort with their soccer game which has to be their best selling game WW non-MGS years(I'm just guessing, I have no idea).
I would say Sega, Square-Enix, Capcom, Activision, Namco, and Ubisoft's support for the Wii have all been from average to great for an unproven system from a company with a proven 3rd place track record. Other arguably big companies like Eidos, Atari, Midway, etc are just churning out trash for everything these days so I'd say they are missing every boat.
I would have to say in the number of sheer missed opportunities EA has to take the cake. The Wii is screaming for a great golf game and EA has the Tiger Woods license yet 12 months and 2 games later they still leave a lot to desire. By the time they fix it We Love Golf and Mario Golf will be dominating. The Wii is perfect for a great life-sim game and we get a 6month rush job. The sequel may be great but it will have no chance against Animal Crossing Wii. The Wii has FPS written all over it and so far the best we've gotten is a PSP port that was only good because the team that made it had only worked on a handheld games and the Wii was a powerhouse to them. Boogie and EA Playground are terrible attempts to quickly cash in on the Wii's casual audience and have no real potential next to GHIII and Mario Party 8. Aside from farmed out Madden 07 all the EA sports games on Wii have been abominations. The balance board has been a known quantity for some time and is begging for a snowboarding/skating/skiing game to be made and we have yet to hear anything from perfectly placed EA (or anyone other than Nintendo) about such a game.
So I wouldn't say EA has missed the Wii boat in the sense that they never bothered to get on but that they missed it trying to get on and are flailing about in the water right now. Also I mean this relative to potential. I know EA is selling a lot more games on the Wii than say Atlas but I'm sure Trauma center has earned Atlas more profit and sold way more than they could have imagined than any of EA's Wii games have earned it.