Here's my list:
NES:
Nestopia 1.36, truly the strongest in my opinion, has all nice filters, 7zip support to select one specific game out of the goodset zips, great compatibility, great speed and sound, great input system (you can set
every key), and good kaillera support. What can one want more?
SNES:
Zsnes 1.51, i like the GUI, great compatiblity, easy to configure, Netplay was sadly taken out for the current release, but if you really want to play online you can play with version 1.42 which is perfectly capable of playing short games like Super Street Fighter 2 etc. but not Monster-Games like SD3.
GB/GBA:
Visual Boy Advanced 1.7.2, once again i think the most compatible, easiest to configure, all around the best, thought sadly also no Netplay.
NintendoDS:
No$GBA 2.4, overall the most compatible, and since the last release finally easier to handle.
Nintendo64:
I prefer Project 64 1.6 over 1964 0.99 though you might want to switch game specificly. There's also the chance if you want to donate 20$ to get the pj64 1.7 beta version which (i guess) is superior to both (as it's still being worked on). Can't tell much about it though.
Playstation:
SSSPSX 0.0.34e! In my opinion this is the best Plugin based Emulator around. It features a very simple and easy to configure design (very straight forward), the ability to make an iso list in the main window (though sadly no different video plugin setup for special games), great speed and compatibility (it's based on PCSX) and most importantly it has full Rumble Support for Gamepads like the Xbox 360 Pad. Give it a try, you won't be disappointed. Other than that the already mentioned pSX Emulator v 1.11 which also has good Rumble Support and compatibility but no plugins/enhancements.
Sega Genesis,32x and SegaCD:
Kega Fusion and Gens32 Surreal imo, though you sometimes have to switch to find the best for specific games.
Dreamcast:
nullDC, was released a short while ago and truly rocks, great compatibility, only problem is there's no Pad Support yet (but you can use Joy2Key, or ControlMK to solve this issue) other than that the best DC emu in my opinion.
Playstation 2:
PCSX2 0.92 for Windows and 0.93 for Linux, what can i say the best PS2 Emulator, simple as that.
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