PAL 480p with component cables looks the best (as PAL displays in 720x480 instead of 640x480) however if you really care about graphics you should just use Dolphin. It's amazing how good games look on it even though they were never designed for it.
The next best thing is RGB SCART but that's no point unless you don't have a HDTV.
Upscalers are overrated and useless, you can't add detail that wasn't there in the first place. Unlike Dolphin it doesn't actually cause stuff to be rendered at a higher resolution, it's still rendered at the same resolution, and it might actually look worse than just letting the TV upscale it (though that depends on your upscaler and TV I suppose)
It's the same sort of thing as 2D to 3D conversion. It tries to do the impossible and doesn't do a very good job at it.