I use NDSTokyoTrim. I recommend using it because:
It detects WiFi games so it doesn't trim off the parts in a ROM needed when you use "the WiFi game"
Easier to trim ROMs (with the R4 one, you have to browse ROMs individual, which is a pain. With tokyotrim, you just tell the program the folder where ROMs are and BOOM! it makes a list.
Compared it to the R4 trimmer. TokyoTrim trims more waste space than R4 trimmer.