in pm:ttyd, the whole battle music is a remixed version of the mario theme, not just the first six notes.
also M&LPiT has the theme in some parts of the mushroom kingdom overworld.
M&LSS has the theme near mario and Luigi's house, which the song is mixed partioally with a smb3 song (1st world map music). - also, i believe mario is humming the theme in the shower