In Commander, if your commander is in the command zone and would be affected by a replacement effect that puts it somewhere else, which replacement applies?

When a game event would affect your commander, multiple replacement effects may apply simultaneously. The Commander rules introduce a special replacement effect (CR 903.9a) that allows a commander to move to the command zone instead of going to a graveyard, exile, hand, or library. If another replacement effect also tries to modify that same event, the affected object's controller chooses which replacement effect to apply first (CR 616.1).

Crucially, the Commander replacement effect only applies when the commander would go to the graveyard or be exiled (CR 903.9a). It does not apply if the commander is being put into your hand or library — those destinations are also covered, but the key point is that the replacement effect is optional: you may move it to the command zone. If you decline, the card goes to the originally intended zone.

When two replacement effects compete (for example, a card that says 'if a card would be put into a graveyard, exile it instead' and the commander rule both try to apply), the commander's controller chooses the order of application per CR 616.1. Once one replacement has been applied, you re-evaluate whether any remaining replacement effects still apply to the modified event (CR 616.1d).

Concrete example: Your commander would die (go to graveyard). A Rest in Peace replacement effect says it goes to exile instead. You, as the commander's controller, choose which replacement applies first. If you apply Rest in Peace first, the commander is now going to exile — and the Commander replacement effect can still apply, letting you redirect it to the command zone. If you apply the Commander effect first, it goes to the command zone, and Rest in Peace no longer applies.

The upshot: in practice your commander almost always ends up in the command zone if you want it there, because you control the order of replacement effect application and the Commander replacement can usually be applied after any other replacement that changes the destination zone.