My current builds do perform per-pixel synchronization of the CPU and PPU. It cuts the speed in half compared to scanline-based, and even that is only because I run the chips out-of-order until synchronization is absolutely required.

It's needed by Air Strike Patrol to draw the plane's shadow, as seen here: http://byuu.org/bsnes/images/accuracy/air-strike-correct.png

It also affects a lot of "line error" issues, but those are fairly easy to work around with a scanline-based renderer.