If you are thinking a mod pack the same way one might be used in Minecraft, you have to keep in mind that most major mods are not really made to be compatible with others. A lot of the well known mods push the memory of Cave Story to its limits, and with the map limit of 95, there would be no way multiple mods could be used. They also may have specific stories, and trying to combine them in one game would result in an odd mishmash of various stories. If you are just thinking a bunch of mods stored together and able to be run independently, then it oughta work fine.