Just to clarify what I'm asking about, it's programs which do the following:


There's a usable example of it
here.
After trying a couple demo versions these were my observations as far as free-hand optimization:
Aseprite: The pixel-perfect option works like the example above and really gives a lot more precision when free-handing small areas. The "contour" tool is also a very handy way to fill in large areas quickly. My only complaint is there's no support for tablet pen pressure, so you can't create line-width variation on the fly.
Pro Motion NG: The trial version doesn't allow you to try the pixel-perfect mode, which is pretty annoying. However, Pro Motion does support pen pressure, so
assuming the pixel perfect mode works just as well as Aseprite's, it's the better choice to accomplish everything in one program. It's simply annoying that you can't evaluate all the functionality before purchasing (the $40 asking price is a lot compared to other popular pixel art tools).
One other factor in Aseprite's favor IMO is the simple GUI; it's a pleasant break from the clutter of mini-windows plastered all over Photoshop. Conversely Pro Motion NG feels pretty much just as bad as Photoshop in that regard.
These are not the only programs with a pixel-perfect option, just the one's I've tried so far.