According to PokeGen which is my goto for gen 4 pokemon editing there are several dozen across all methods documented at the the time of it's most recent release. (there is no way i'm typing all that into a spreadsheet :P) AFAIK method 2 and 3 are common to emulators and have basically never been confirmed on og hardware. for more info check this smogon writeup
Have you tried opening the edited save in pkhex after exporting it to check if the changes are seen by it? Did you make sure to click save in the items window?
For gen 1 and 2 you can use pikasav. For gen 3 you can use a-save by kazowar. For gen 4 and 5 you can use pokegen by codr. All of which are available in the downloads section. If you want to edit more than pokemon and items I don't think their is anything public to do so except a mystery gift injector for gen 3.