Try DeSmuME. This one can be set so you have the 2 DS screens alongside each other at full resolution with graphical smoothing. Of course, you can have the screens arranged just like the DS and it does not look bad at full resolution, it looks perfect.
It has so many great features and I actually have much more fun playing on this emulator than I do on any of my DSlite / Phat units. Be warned that DeSmuME needs a really decent system to get good results but NO$Gba doesn't. I play DeSmuME on my laptop but that has an i7 processor and a 1Gb Nvidia GPU. I get around 60 fps with frame skip set to 1-2.