My list is basically the same as rainwarrior's:
1 - FCEUX for debugging, hacking, studying effects, and so on. It has a shitload of debugging tools that make almost any task simple. I consider it very inaccurate though.
2 - Nintendulator for when I need to debug something that relies on more precise timing and/or video emulation. It gets second place because the debugging tools are fewer and not as versatile as FCEUX's. Nintendulator could seriously benefit from more display options too (IIRC you can't even disable the bilinear filtering, which's extremely annoying).
3 - Nestopia for playing. Very lightweight, easy to use, and one of the most accurate when compared to my actual NES consoles. Has the best video output IMO, when using the NTSC filter.
I have been gradually increasing my use of FCEUX for playing though, maybe because Nestopia is finally starting to feel outdated (I don't keep track of the more recent unofficial versions). After configuring the NTSC filter in FCEUX, I'm quite pleased with the picture, and its inaccuracies aren't really noticeable when playing.
I did try some of the newer, actively developed emulators, but some of them felt really bloated (the multi-platform ones) and others required me to install stuff (C++ runtime, .NET Framework, etc.) that I either didn't feel like doing at the time or my Windows 7 simply refused to install, so my experience with those emulators is very limited, and the first impressions weren't the best.
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