Honestly I don't think there is any besides the map sequences in Super Mario 3. Just curious though. Would be interesting if there was a Super Mario game out there like Super Mario RPG where Mario can jump in all directions. I know once SM64 came along that set the standard for it. But what about before this? Thus far this is all I could find: http://www.virtual-boy.org/vbmarioland.htm
I think you might be able to consider a few of the Cameo's at least higher than shoulder perspective. But there aren't really any gods eye Mario titles I can think of.
That reminds me, there are some Mario Educational titles that have 3D in the SNES versions. Does anyone know if the NES releases of them did any top down perspective? I have only played Mario's Missing really, for the NES releases of those Educational titles. Its still side view but does get a bit of depth going from the northern to southern streets or back. Its not really enough for me to consider it a near miss. Not on the NES anyway.