The Tablet 83 Project will have all the features you'd expect from a graphing calculator on a computer, but coded to be as easy to use as possible. One such case is (over)use of straight-text input for math, vs. emulators which may map delete to sin(. Another example of computer-friendliness will be tracing graphs via mouse position relative to grid.
Other basic features (not necessarily implemented as of this post):
-No ROM requirement
-Program editor
-Program import from binary file