Shastar, I'm going through the RaceIssues lua file now. Ignoring the obvious things like riots on the planet, dropping bombs, etc.:
Planet Activity - City Planning:
Humans and Refugees (and I think only humans are refugees at this point) get +20 happiness if the planet activity is city planning.
(To the devs, there is an "or" in the statement, and confirmed in a game. I understand that humanity is desperate to rebuild, but I think it would make a lot more sense if refugees got a large boost, but normal human colonists got a smaller +10 or +5 bonus.)
Planet Activity - Research:
Refugees are unhappy if you are doing research. They want places to live.
Orthin are nerds, and get happy when the planet is devoted to research.
Planet Improvement - Lab:
Orthin, it cannot be said enough, are nerds. If I am reading the table right, they get +5 happiness per lab on the planet. The morale message changes if you have 1-2 or 3+ labs, but it looks like the happiness is +5 per lab.
[EDITED] Planet Improvement - Markets:
Phidi are mercantile, and get +5 happiness per market on the planet. (This is not handled as a special morale modifier, like the Orthin's lovable nerdiness, but is simply an addition to the market's happiness calculation. So, you don't see a pop-up for this, the numbers are just different.)
(I'm going to experiment with giving a similar but smaller bonus to Spice Mongers.)
These bonuses do NOT depend on the empire. If you acquire Humans or Orthin, you can use City Planning or Research / Labs to make them happy.