A lot can be written about this, but I'll just place some links and make it short.
BLT-research
The link http://www.bltresearch.com/published.php contains 3 scientific peer-reviewed articles.
Eltjo Haselhoff
There are more from a dutch scientist Eltjo Haselhoff , showing that the anomalies in the circles match with a source a few meters above the circles in many occasions. It continues with the conclusion that the balls of light above the cropcircles might be these sources.
This is some of his research:
http://www.dcca.nl/experimental-study.pdf
http://www.cropcircleconnector.com/anasazi/deepening2001.html
http://www.swirlednews.com/article.asp?artID=185
Sceptic scientists
I have never seen peer-reviewed scientific papers that show that these are manmade. I've seen many not-properly peered reviewed articles in popular scientific magazines that claim that they are manmade, but they don't match with the observations.
This movie with bad sound-effects gives a reasonable but still sceptical overview of the current state of the science on cropcircles:
https://www.youtube.com/watch?v=ZLg20skt6WA
(updated link)
Conclusion: they can't duplicate the anomalies. The pseudo-skeptic scientists keep on trying to replicate them, but think they will be able some day. But they won't....
Other scientists
It may amaze you, but there are many scientists that have researched cropcircles and have found interesting differences between hoaxed cropcircles and genuine cropcircles.
Then what makes the cropcircles?
My own theory is that the anomalies that we find in cropcircles are related to "chi". Chi or Qi is widely known (as life-force) and in concentrated form it can produce all the anomalies that we see in cropcircles. The only problem I have in proving my theory scientifically is that science does not yet accept the reality of chi, partially because it has so many different forms. There are a lot of people working with it, and many (like me) can clearly experience it.
The presence of chi does not directly mean that a cropcircle is genuine, just like a footstep in a cropcircle does not mean it is a hoax.