on the afflictions page is says a comatose creature cannot be woken by any means, but is there any way to wake a creature rendered comatose by eyebite, sequester, or similar methods?
Since the section you are referencing refers to alternate rules for dealing with Poison and Disease conditions provided by Pathfinder Unchained, the answer to your question is to find a way via "eyebite, sequester, or similar methods" to inflict sufficient exposure to poison or disease so that someone succumbs to it and produce the state. Assuming, of course, you are playing in a game that is using that set of rules from Pathfinder Unchained.
Comatose is not a standard Condition in the game. So, you will not find a spell, class feature, or special ability that imposes it as a condition since it is NOT a condition that the standard rules use.
I think you will see clearly in the section from Pathfinder Unchained that they are proposing a new method to handle the consequences for diseases and poisons, and only use the term in that context. It was not a mechanism that I had looked at closely before, and I find it interesting, so thanks for bringing it up.
The condition exists in the CRB but is only defined in the eyebite spell as near as I can tell.
Comatose: The subject falls into a catatonic coma for 10 minutes per caster level. During this time, it cannot be awakened by any means short of dispelling the effect. This is not a sleep effect, and thus elves are not immune to it.
"by any means" is pretty comprehensive. Removing the effect is the only think I can think of that will work.
but is only defined in the eyebite spell as near as I can tell.
Good catch!
I think that reinforces the idea that it is not a standard effect, but a specific outcome of certain events, e.g. a spell effect, and (with Unchained) certain diseases and poisons. I actually think it would be a good standard condition.