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I a while I've been experimenting with the video and audio settings with ZSNES and Snes9x. I'm hoping that someone here knows more about this stuff than I do but here's what I think the best settings are:

ZSNES Video
1024x768 DS Full Screen (can be any resolution)
Triple Buffering
Super Eagle Engine

ZSNES Audio
44100Hz
Sound Buffering
8-Point Interpolation
Hi Quality Lowpass

Snes9x Video
AnyxAnyx16 resolution
Super Eagle Filter
Render in 16-bit
Transparency Effects
Hi-res support

Snes9x Audio (ain't worth it imo)

The only real strength of Snes9x seems to be it's windowed mode because ZSNES seems far superior in every other way. With Snes9x I can play while watching CoN chat but I don't even bother with the sound. It sounds terrible for some reason whereas ZSNES does a good job emulating the sound (a little crackle in the music here and there but overall pretty close to the real thing). Just in case you guys haven't messed with these settings you should give it a shot. I think the Super Eagle filter is great and makes FFVI look a lot better. Does anyone else have suggestions for better emulator quality?

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FFXI (Siren server)
Tauu the Windurstian Tarutaru!
White Mage & Paladin

Sound should be at 36000Hz with Gaussian filtering for accuracy, though changing it to 44100Hz or 48000Hz may sound better depending on your sound card, since it tends to get filtered to that before output anyway. It just depends if you prefer the sound driver's method or ZSNES's.

Only enable low-pass filter if you don't have this in your sound hardware. I was reading that a lot of sound cards or speakers do this for you, so doing it twice isn't really optimal, but I wouldn't know how to tell.

If Snes9x sounds bad, try checking the Anti Resonance checkbox in sound options. It sound core is less accurate than ZSNES, I think, but it is improving. The current Snes9X release sound might be better than the last ZSNES (non-WIP) release's; I'm not sure, and it probably depends on options I don't know because I don't use it any more.

You can run ZSNES perfectly well in a window, though the 1.36 release won't let you use D-modes (allowing filters like Super Eagle) unless your desktop is in 16-bit instead of 32-bit. This is fixed in the WIP builds, so maybe try one of those. But I certainly agree that using the S rather than R modes is the way to go -- R may give you a more accurate output ratio compared to original SNES pixels, but the picture never would have looked that way on a 4:3 TV set. SNES pixels should always be wider than they are tall.

Super Eagle and other graphic filters are a matter of personal taste, and what's optimal for one person might not be for another. I personally don't like the rounded edges Super Eagle gives at all. I stick with just Hi-Res Mode 7 in the D modes, but there's a problem with this: if your video card doesn't do an automatic bilinear filter on the stretched image, you tend to find that the approximation is bad and you get some lines of pixels wider than others. In this case I would just use the bilinear filter option, though this makes things more blurry than a native bilinear stretch does in D modes (though it looks pretty much the same as the native filtering on non-DS modes -- and if you want to test whether native filtering happens, try an S mode without D and see if you get a blurring effect). HQ2x/HQ3x are probably the best of the Super Eagle style filters, but they're also only in WIP builds.

One last tip: when you're playing in full-screen, try and get your refresh rate at 60Hz. Normally I'd recommend higher, but you'll find the SNES picture much smoother at 60Hz as the SNES picture updates in sync with the refresh rate (enable triple buffering for this, too). Doesn't work for PAL games, of course, which want 50Hz, but you can find an NTSC version of anything I think. In theory, 120Hz and 100Hz should be possible on the same principle, but it doesn't work properly; there's a ZSNES mode called KitchenSync which you can activate on the command line which is supposed to do it (-K or -KS I think?) but I can't get it to start up that way.