I distinctly remember starting on inverted-Y thanks to Star Fox 1 (and never had to deal with this with genres like FPS because I play them almost exclusively with a mouse and keyboard), but whenever I pick up newer games with flight controls, for the first stretch I always wind up swapping back and forth between inverted and standard as neither of them feel quite right. I remember having this problem with the SF64 remake on 3DS, and I think I settled on inverted, but I'm not really sure; something was off about it.
I never invert with KB+M or gyro, which is how I play all my FPS or TPS. I can't wrap my head around how inverting those would work. I have zero recollection of what I used for single-stick shooters like GoldenEye or RE4. I'm not even sure what I used in Metroid Prime when I played the hell out of it back in the day, as I've had no reason to go back to it on GameCube since Prime Trilogy on Wii delivered motion controls.
As far as right-stick camera controls are concerned, I use whatever setting matches Wind Waker. I'm not convinced that game settings are consistent about labelling this, on either axis, as normal or inverted.
You know what: I just function better in 2D.