I like Robert Broglia's ".emu" series. I use those for Atari 2600, NES, SNES, Gameboy, GB Advance, and Genesis/Master System. They run great, have a lot of options, and I like having the same interface for most of my emulators.
Nostalgia.gg for Game Gear, DraStic for DS, and ePSXe for PS1.
As for N64, I have N64oid and Mupen 64 Plus AE. They each have their strengths and weaknesses, but there doesn't seem to be much progress on the N64 front... If anyone knows of something better, I'd love to hear about it.