Rioting Citizens

troops on planets will keep up order and support happines
you´ll need 50 to 100 troops on a planet to have a positive effect (at least that´s what worked for my planets so far).

i think you can also research some of the cultural techs, one of them should add something to happines.

I would suggest just attacking the enemy, you don't need to decalre war on them, just thin out their fleets a bit, this will reduce your negative modifyers. This will lower your standing a bit with the empire concerned but as long as you don't destroy or capture any colonies they probably won't declare war on you.

You also need to be aware of what goverment you selected as this will affect your planets loyalty and happiness in these situations. You can also build Pacification centers (off shoot from Applied Political Science) to MAKE your people happier.

cordas,
Those "Pacification Centers" kind of remind me of the classic movie "A Clockwork Orange". I can just see them connecting up those eyepieces and giving them their "psycho" therapy to keep them calm.
Omnius

Shakerfish,
Have you checked your intel screen? I'm wondering if you're the victim of some AI intel ops. You can see if the AI's are using intel against you and how successful their intel ops are. That could be the reason your people are going ballistic.
Omnius

Funnily enough I get exactly the same feeling, hence I try to avoid using them at all costs.

I will happily sacfrifice my own people but don't like to pacify them..... Go Figure.

The "Pacification Center" could be anything from a sports stadium to something like that. The language, and description, seem to be intentionally kept vague to let you imagine it yourself.

But mostly, your citizens do not like unfriendly aliens traipsing about their space. That sort of thing should make you antsy, so why shouldn't it make them?

Tip: The AI seems to be very easily convinced to go someplace else by mines. Just drop a few mines on a warp point, and after they hit them once or so, they'll stop going that way.

As opposed to the human player, who will just warp in a few obsolete scows first as Polish Minesweepers.

Happiness and Loyalty seperate are affected in different ways though there are some conditions I think that are parallel...

Apparently the conditions of a planet affect Loyalty. The nicer the conditionals, the slower the loyalty disintagration. Hitting up the Cultural Improvements and choosing a particular government at start adds up. I am currently experimenting with Condition Improvements on my more disinfranchised colonies.

I place a suititable garrison on a colony shortly after settling it. The total weight of troops on all planets in a systems I believe addes to total System Happiness, or at least that's the way it is reported on the News updates. I haven't had a colony under Jubilant for the majority of my current 200+ turn game. You just have to head it off early before it compounds into a problem. Once a riot starts its hard to quell.