In no particular order ( mostly cos i think ranking beyond a certain degree of precision hurts the art involved ):

• NieR Automata
• NieR Replicant (ver 1.22… , realistically)
• The Talos Principle ( one of the most suprisingly brilliant games that too many people haven’t played)

then i suppose one tier below, not consequent of any particular shortcomings, but rather just not being at the same “transendent” level as the above:

• Crosscode
• Citizen sleeper
• What Remains Of Edith Finch
• Portal & 2

NieR automata literally changed my life, so it kinda deserves it’s own top spot, but placed as is in spirit of the question.