Hey, loving the game, just still trying to wrap my head around a few of the concepts. Right now, I just want to make sure I understand this right:
If I have a planet that is ultra rich, and gives 8 industry per worker, but also has a worker penalty of 50%, then each of my workers only produces 4 industry, right?

Unless you have a Morale or Labour bonus from a Leader, Tech or Government type.

Alright, so each "happy" morale mask on the planet reduces the penalty by 10%, right? And is the penalty just to industrial workers, or does it effect farmers / scientists too?

Actually, each happy mask is a 10% bonus, however I can't tell if it is additive or multiplicative. The text in the manual says: "Each smile represents a 10% bonus to production...".

There are worker penalties from all sorts of sources. If you're playing a low-G race, you get a significant (50%?) penalty to all production on non-low-gravity worlds. Most races, if they have no marine barracks or better, take a 20% morale penalty. And so on.
I think that morale penalties apply to all production, including food and science, not just industry. I just tested it (started a new game and colonized a non-low-G world) and gravity penalties DO apply to research.
If you click the morale bar, it tells you how much of a penalty/bonus you're getting. 20% penalty is for planets without barracks. A barracks, or a Unification government, brings it up to zero. Morale bonuses come from entertainment buildings and apply a percentage boost to everything.

Alright, very good to know - thanks everyone!

If you're Low G it's:
25% on Normal
50% on Heavy G

If a planet says "-50% worker penalty" is that a bonus to worker production?

All PP produced by workers, so not those from recyclotron or auto factory and such, are halved. This is bad, of course.

A negative bonus.