A system-agnostic question is not related to any one particular system of rules.
In general, questions should be about the problem you face, and if you have an issue within a specific game system you should ask within the context of that game. Do not widen your scope to "make it more useful for others," you question and answer(s) will be more useful if it is more focused.
However, there are some issues which transcend specific games/game mechanics and, in that case, can be tagged as system-agnostic. This conveys that you are looking for solutions not directly tied to a game's mechanics, or that you are but don't care what.
You don't really need to use a system tag at all in many circumstances. "How do I deal with a player that shows up late" doesn't need to be explicitly tagged system-agnostic. It is instead a signifier for something that happens in game but that you are looking for techniques not rooted in a specific set of game rules.