Have you tried out the
FCEUX SVN builds? I get mine
from EmuCR. Note: the FCEUX configuration file between non-SVN and SVN (as of this writing) are not compatible, so you will need to "start fresh". Sometimes they become incompatible between SVN builds too, so be aware. When you find settings that work well for you, *write them down*.
I've never been able to get fully smooth ("non-glitchy") output in FCEUX visually on Windows 7 Ultimate. There is always some degree of stutter, albeit intermittently. I've just learned to accept it, as I use FCEUX predominantly as a debugger/development emulator. These are the settings **I** use for **my** setup, using purely windowed mode, with a strong dislike for blurry (anti-aliasing or bilinear filtering) output (i.e. I prefer pixelated output):
Config --> Sound --> Output/Output Format:
* [x] Sound enabled
* [ ] Force 8-bit sound
* Quality: High
* Rate: 44100 Hz
Config --> Sound --> Buffering:
* [x] Use Global Focus
* Sound Latency: can't tell (no counter/indicator), but might be 20 or 25ms
Config --> Video --> Full Screen Settings:
* [ ] Full screen (Alt + Enter)
Config --> Video --> Windowed Settings:
* Size Multiplier: X = 2.000000, Y = 2.000000
* [x] Force integral scaling factors (when resizing the window)
* Special filter: none
* Sync method: none
* DirectDraw: Hardware acceleration
Config --> Timing:
* [x] Set high-priority thread
Config --> PPU:
* Old PPU
There's literally zero way to guarantee this will work for you, however. Video card drivers, video card chip, power profile settings (in Windows), Aero vs. Basic vs. Classic (in Windows), windowed mode vs. full-screen (in FCEUX), sound chip, sound drivers, and even some BIOS settings (things like SpeedStep or Cool'n'Quiet, and CPU C-states) are all contributing factors (yes, even the sound aspect -- a lot of people get clicky or stuttery sound sometimes depending on if things like Vsync are enabled or not). The number of variables are even more than that, so really it boils down to "figure out what works best for that specific computer".
In general, FCEUX does not make for a "good play experience", but makes a pretty damn good debugger/development environment. I actually prefer Nestopia UE for actual gameplay, although on Windows 7 I've never gotten its windowed mode to be smooth (it'll occasionally show some tearing or skip a few frames) -- while the exact same emulator/settings/everything worked smooth as a baby's butt on Windows XP. I gave up trying to accomplish smooth output of this sort -- it's an uphill battle that can't be won, as there's just too much BS going on. Full-screen mode is a completely different story, however.
I can't help past this point. Good luck!