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I wonder who is responsible for security on an airplane, especially on a flight within Europe. In some countries (e.g. USA) sky marshals counter hijacking, but I don't know if a similar practice exists in European countries.

The incidents (in this question) are not limited to hijacking. Say a passenger's behavior is aggressive, he/she may hit someone else. What agency and staff are primarily responsible for in-flight security?

Ultimately everything that happens on a plane is the captain's responsibility. But in practice, if a passenger is unruly and does not follow cabin crew instructions, cabin attendants can and will physically restrain them (many airlines carry plastic cuffs or zip ties for this purpose), with voluntary assistance from other passengers if needed, and then hand them over to police at the destination.

The flight crew is in charge of security and passenger control once the plane is airborne. They are equipped with passenger restraint devices (handcuff type zip ties and such). I have witnessed unruly passengers being restrained during the remaining duration of the flight.

OP: Who would deal with this incident?

The cabin crew.

A 'violent' passenger on a plane from Dubai to Heathrow was restrained by four cabin crew and a policeman after allegedly launching a terrifying mid-air attack on staff.

https://www.standard.co.uk/news/uk/passenger-restrained-by-cabin-crew-and-police-after-midair-attack-on-flight-from-dubai-to-london-a3180616.html

Or other passengers.

A drunken British was restrained by four passengers on board an easyJet flight and dragged off the plane on his knees after attempting to open its emergency door at 30,000ft.

http://www.dailymail.co.uk/news/article-3483547/Drunken-British-man-tried-open-emergency-door-EasyJet-flight.html

Regarding Air Marshals, we tend to prefer preventative measures here in the EU, so better pre-boarding security checks etc to weed out any actual serious attempts at hijacking in the air.

Pretty much everything you hear about these days is alcohol related, and can be dealt with by trained onboard crew members.

By the book, it's the responsibility of the air marshals (if available) then the cabin crew, but in reality able-bodied passengers are usually involved to help. Usually police officers, firemen, etc. (if were around) volunteer to help without asking them after identifying themselves.

Why are passengers involved? it's actually allowed for cabin crew to ask for the help of the able-bodied passengers in cases of emergencies, unruly passenger is an emergency.

Regarding flight deck crew, policy usually requires them to lock the flight deck door for any kind of access in such cases until things are cleared out to make sure it's not some sort of a diversion to allow potential associates to do a more serious offense, that is hijacking! By locking flight deck door I mean even authorized cabin crewmember(s) will not be able to access using the designated code, which they can in normal cases.

Once there's an unruly passenger onboard, there's a form to be filled by the senior cabin crew and signed by the captain to be handed to the authorities after landing. The captain will usually contact the nearest airport once the case is reported by cabin crew, then the captain will decide whether to land immediately in the nearest airport or to continue the flight. Either way, the passenger will be handed to the airport security once landed. Usually passengers will be requested to hold deplaning until security has detained the unruly passenger.

Source: I'm a cabin crewmember.