Tough call between Nintendo and Capcom. A year ago, I wouldn't have questioned it, but I've been playing some of Capcom's NES games (Gargoyle's Quest 2, Sweet Home, Little Nemo: The Dream Master), and they're just fantastic. Both have a huge backlog of classics. Both have made some great games this generation. Both are the best reasons to own a Wii*. Hmm...I might still leans towards Nintendo, but a good Breath of Fire reboot could change that.
Edit: Upon further thought, that's highly debatable. Capcom, Sega, and Konami (I need to check out that Rebirth series on Wiiware...) have all made several great games for the system.