video filters can now be used.
currently, to select one, you need to go to "Settings" --> "Video" --> "Video Filter" and select a ".filt" file, those files are available in the latest nightly archive in retroarch/filters/ .
I would recommend just copying the "retroarch" folder from the archive to the root of your SD-card, and then setting the "Video Filter Dir" (in "Settings" --> "Directory") to "sdmc:/retroarch/filters", that way you can get the available filters listed directly from the "Video Filter" option.
to disable a filter, just press "start" when the "Video Filter" entry is selected. ( "start" is the default hotkey for setting back any config value to the default one).
and as
@Steveice10 already pointed out, those filters are quite CPU intensive, so expect a huge performance penalty when using them, and also, don't expect much from them due to the very low resolution of the 3DS screens. (the accessible resolution at least, things would become far more interesting if the full 800x240 resolution of the top screen ever became accessible).
also, I didn't test all of them, so some might not work correctly/at all with some cores.