Hallo. I just found out about this particular NES emulator, which seems to be somewhat lesser known, currently. But my first impression, at least, is that it seems to be one of the best out there.
Anyhow, I actually came here to give some feedback, too.
1#
It would make sense if you could go full-screen and keep the scale factor intact. Like, if I want full-screen on 1920x1080 with 4x scale for perfect scan-lines. I can't seem to do that currently, unless I'm missing something.
2#
A borderless fullscreen mode would be nice. Or at least a way to hide all borders/interface. Then it should be simply enough to use a third party tool to achieve it. The reason why it would good is simply that borderless is a good alternative to using vsync, if you like it more. There's different trades offs to them.
3#
I haven't come across an NES emulator that can play the title 'Little Nemo - The Dream Master' to my complete satisfaction. One reason is that the game requires chopping in most sides of the screen. A couple of emulators that do this. And puNES provides the tools for this, great.
However, the game also has an annoying flickering glitch line between the game world and the game's interface. When the emulation is running this line is a real eye catcher because it contracts/expands continually. I like for a way to hide it.

The only NES emulator that I know of that fixes this glitch is JNES. However, that particular emulator only has left side 8px chopping.
So here's an opportunity to beat all of the others in this particular case.