For the moment I think that Jin is the father, but agree with the above posts that Sun was probably more than 'just good friends' with Jae at some point. Sun's conception could be another pointer that the island has healing properties - like giving Locke his legs back - but I'm still having trouble completly buying that, and think that there is a more scientific explanation for it.
But it is an interesting point where the pregnancy kit came from: it could have been from the plane luggage, but if you thought that you may be pregnant I for one would check it out straight away instead of carrying a test with me to another country! I think that it probably came from the hatch, and was part of the supplies that came with being on hatch duty just in case the two people down there were a girl and a guy...and it does seem that Dharma could have another link with another company because the pregancy kit said Widmore labs on it.
There could be a possibility that Sun could have been used in a child related experiment, but pinpointing the time when that could have happened is difficult! It will be interesting to see what happens with Sun's pregnancy, but I bet that we won't hear much more about it until Season 3!