Definitely-- the entire "Famicom Wars" series (Advance Wars to us, but it's been out in Japan since the NES) is great.
If I had to choose the best 1st party Nintendo game, it would be impossible. New games and new versions of older games are constantly coming out.

Super Mario Bros 3 is probably right up there in the 'Best of Nintendo' category (which automatically means "Best Games Ever"). The game is pretty darn perfect.