What determines whether actions are good or bad? In a large number of religions, 'good' and 'bad' are defined by some all-powerful diety who either sends a representative or himself to tell us about what exactly they want us mortals to do.

In Buddhism, instead an enlightened individual basically worked it all out.

So the basic question is - why does that happen? What decided that killing (even if your intentions are good*1) will cause something negative ? What about the other actions? There is no 'final judge' to confirm or deny we've followed a particular path - so why does the universe (?) act this way? And what makes us sure that we're correct?

*1 - It's an impression I got from reading some other answers, if I'm wrong on this please do correct me)
In Buddhism, the concepts of good and evil do not exist as in other religions (no being is inherently good or evil). No deity tells you what to do. There are the teachings of the Buddha, that we can make use of, as opposed to believing in a doctrine (such as "Ithe authority tells you this, therefore you should obey*"). 

However, there is still a distinction between the helpful and harmful, skillful and unskillful - in the context of the path (to liberation, nirvāṇa, nibbāna). In terms of karma (actions, kamma), there are the wholesome and unwholesome, but these are useful in terms of the actions we choose to avoid and to act on, in each given moment (now).

Mara, as mentioned in the Pali Canon, is referred to as evil (in the English translation), but even he will be enlightened one day. In other words, noone is inherently evil (or good) - no deities, ghosts, humans or other, in Buddhism. For instance, Maha Moggallana, disciple of the Buddha, mentioned to Mara at one point that in a previous existence, he had been Mara, and (the current) Mara had been his nephew. Strikingly, despite having been the "embodiment of evil in the world", a number of lifetimes later, he was one of the prominent disciples of the Buddha (Gotama).

An excerpt from the story: (source)


  The first Buddha appearing in our "fortunate aeon" (bhadda-kappa) with
  five Buddhas, was Kakusanda. He lived when the lifespan of man was
  40,000 years and when the first darkening of the golden age became
  evident because of a king's lack of concern and the occurrence of the
  first theft. Because of that, man's vital energy became reduced to
  half. At that time, Moggallana was Mara, chief of demons, lord of the
  lower worlds, and his name was Mara Dusi. He had a sister by name of
  Kali whose son was to become the Mara of our age. Hence Moggallana's
  own nephew was now standing in front of him at the door post. While
  being the Mara of that distant time, Moggallana had attacked a chief
  disciple of the previous Buddha by taking possession of a boy and
  making him throw a potsherd at the holy disciple's head so that blood
  was flowing. When the Buddha Kakusandha saw this, he said: "Verily,
  Mara knew no moderation here" — because even in satanic actions there
  might be moderation. Under the glance of the Perfect One the astral
  body of Mara Dusi dissolved on the spot and reappeared in the deepest
  hell. Just a moment ago he had been the overlord of all the hellish
  worlds and now he himself was one of hell's victims. A moment ago he
  had been the greatest torturer and now he himself was undergoing one
  of those terrible torments.


Whether we believe in the details of the stories in the Pali Canon is up to each of us. However, important to note, is that we all have the ability and opportunity to choose a wiser path.

Regarding your questions (in shuffled order):


There is no final "judge". No being (God or otherwise) controls our existence.
The Buddha (through long practice) awakened to (discovered, if you will) the way things are, how this existence functions.
Upon awakening, the first inclination of the Buddha was that "noone will ever understand this" - that it's impossible to teach. However, he was persuaded that some beings could be helped, and so he decided to teach others.
Briefly explained, words are inadequate to explain the way things function (karma, and so on), so instead of preaching something to believe in, the Buddha pointed the way for each of us to find out.


So noone "decided that killing is negative" (nor did anyone decide the effects of other actions). However, Buddhists will gladly help you on the path to finding out for yourself, to discover the effects of karma (your actions). Regarding being "sure we're correct", don't just take anyone's word for it. Try it out, see for yourself, do the methods and teachings from Buddhism work for you. Only then can you find certainty.