Nintendo NES

The best current one (2019) seems to be fceux. It has full-screen OpenGL support which provides nice smoothing. It has some bugs though; for instance NTSC does not work in full-screen, another mode must be chosen.

Previously used

fakenes is good, with an excellent GUI and an excellent video support via OpenGL. But recent ebuilds do not compile, and the software seems abandonned.
Fakenes is quite slow with good video options (HQ4X). It also must be ran in windowed mode in order to use alt-tab.
Mednafen is another candidate. Recent versions are not available in Portage.

The best one on Linux seems to be Yabause. Although slow, and problematic for sound, it is impressive already.

You must use DOSBox. I did not find yet a good front-end for Gentoo. Write the configuration file yourself, and start the emulator directly on the command-line with as an argument the .EXE you want to load.
Press Control-F10 to turn the mouse cursor off (useful for many games). Press Control-F11 or F12 to increase or decrease the CPU cycles. Some old games may need a very low cycle rate. Beware that by default these keys are already captured by KDE.
Press alt-enter to switch fullscreen mode.

Important settings are fullresolution=desktop and windowresolution=desktop. If fullresolution=original is used, the resolution used for DOSBox will be the one of the game (eg, a very low one), but the graphical chipset may smooth things out and it may turn out to be a correct rendering.
If windowresolution=desktop is used, the rendering engine should support scaling. This is the case with OpenGL, but on Gentoo I cannot seem to get OpenGL to work correctly.

Vice 1.22 is good, however I had problems with keyboard keys and speed (while reading the disks).

Excellent emulator to play LucasArts games as well as other ones such as Legend of Kyrandia.
Don't select the ALSA driver as a sound driver (for some reason it then says it cannot find the MIDI port). Select the Adlib driver or the default one.