For questions that are explicitly not restricted to any one particular system or rules, where the asker wants solutions to the question that are not directly tied to a game's mechanics.
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"; in most cases, your 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. For instance, "How do I deal with a player that shows up late?" doesn't need to be explicitly tagged system-agnostic. The tag is instead a signifier for questions about something that happens in-game, but when you are looking for techniques not rooted in a specific set of game rules.
If you're still unsure of this tag's usage, check out the relevant FAQ.