I will do 1:1 pixel ratio if I can, but most times I end up squishing the screen. I like in nesDS how I have the option of doing both. I can tweak where the screen is vertically, and squish/stretch. I end up doing every game manually, you'd be surprised at how many games waste space at the top and bottom. I'm playing Faxanadu now, and it looks quite good, I can see everything on the screen I need to. I also prefer aLerp filter to the standard flicker.
CATSFC is the best SNES emulator for DS, what makes it so good is it uses the CPU on the Supercard DSTwo. What I don't like about it though is the 4 or so set screen adjustments that show the middle of the screen, top part with the bottom cut off, bottom part with the top cut off, or scaled to full screen. I mean everything is there... but I miss the fine tuning nesDS provides.
i really like the video options that nesDS has, too. but is there a way to save individual settings for each game? i havent tinkered with it that much, and neither with the filters.
anything below 1:1 will drive me crazy for pixels get squashed.
i dont really know what you mean about the CATSFC settings, but my DSTwo should be arriving this week so i will try it out.
also, like you said about SNES games to GBA ports,
i might prefer to play some GBC versions to the NES originals when on the DS,
so just a heads up, for Super Mario Bros, the best version of all time is the Deluxe one for GBC,
i actually own the cart and to me it's actually better than other versions of the game,
it includes the whole first game adjusted to the GBC resolution,
with a save feature, and the secret
continue feature that was hidden in the NES version, PLUS it include the
whole Super Mario Bros 2 Lost Levels once you beat the first, which wasnt even released on NES outside of japan.
it also has a mode where you look for hidden coins and eggs while doing the levels, kinda like donkey kong country coins, i really liked that and felt it woulda made a good addition to the original game, aside from that it has a time trial race mode with difficulties, which gives the game some variety, and i dont know if anything else.
kinda out of subject, but since we were talking about ports when playing on a handheld, i felt obligated to mention that one, if you havent looked into it, do so