[ElijahTW]

Is there any (free, if possible) programs that can apply filters like those found in ZSNES to an image?

Maybe there is even a photoshop plugin? Or even possibly there is such a feature built into photoshop that I don't know about

 

[Hard core Rikki]

A few of these filters exploit the multiple layers to give nicer results.
I believe there's a GIMP filter, and an Mplayer one IINM (not sure about multiple layer support, but being filters instead of commandline bats, it should probably look similar to the regular filtering from inside emus).
Of course you could just drag and drop pictures onto a commandline converter like the demo one for hq4x (which outputs a resized filtered version of it).