The primary established mechanism for safe softforks is the reserved script NOPs (which will not be relayed or mined by unmodified software today), the secondary one is transaction versions. They are reserved for explicitly this purpose. The reason for this ranking is that version is global to all inputs and outputs in a transaction; which creates unwelcome tying-- one should be able to spend and create mixtures of coins under different rule sets. For changes that happen outside script, however, version is still available for use.

For segwit the primary mechanism will be segwit witness script versions... which are more clear and flexible than the reserved NOPs.