I think most work at this scale tends to be contract-based, payed per-project or milestone, but it depends on the structure and size of the company.
Mojang is indie, although large with lots of money, and they have proper employees. 2-3 guys working out of an apartment bedroom, almost certainly haven't got any real money to throw around (the kind of place that, if you went to work for them, you'd have to bring your own soda and hotpockets). Indie studios range the entire gamut inbetween, but most of them are probably nearer to the latter than the former if they don't have a publisher or even a VC.
Just to throw some numbers out there, after college I worked my first software job for the probationary (6mo) rate of something like $24/hr, they were a small (~20 people) company that customized software for other businesses and sold seat-licenses to said software, it wasn't gaming related. After that job, I had an offer from a fairly well-established developer who's business was essentially to crete games for big-name 3rd-party IP that was handed down from the publisher -- I think the salary they offered was equivalent to $37/hr, and they didn't offer much else in way of compensation (no signing bonus, stock, etc), except for what was a relatively good health insurance package. I ended up not accepting that position to take a non-gaming position that offered better pay and work-life balance.