It's a personal thing, whatever feels comfortable for you. However, the higher the bar, the less efficient pedaling is and you have to pedal harder. Also, more upright position may not be good for your spine. I know, it's counterintutive but riding with a straight spine causes it to compress from shock and sending the shock up, through the discs (bones), which is really bad, rather than bend and flex like a spring and dissipate the shock using the muscles as suspension. And even the softest saddle and bike suspension can't compensate for that.

For most people the best position should be when the bars are around the same height as the saddle, assuming the frame is sized correctly.

If your back and neck hurt from riding, don't raise your handlebar above your seat level, it'll likely make it worse in long-term if you ride a lot: make sure the bike is fitted properly and work out a bit to strengthen your back muscles and increase flexibility. Of course, unless you have a documented health problem and your doctor gave you specific instructions.

And yeah, I also like adjustable stems. You can change the height during rides to suit your needs.