I am a student in South Africa but I am not from there, in fact, I am from The Netherlands. I would like to know if I can get a visitor's visa twice for 90 days, having the first one expired I want to know if I can just enter the country again without applying for another one which takes a long time. I have been waiting for my study permit for ages and can't just be out of the country without attending classes.
I can't seem to find anything that says you can't, and it would be highly unusual if you couldn't. The exemption you get as a Dutch citizen allows you to enter SA without a visa as you know, though the rules of your stay seem to be the same as if you got a 90 day visitors permit under section 31(3)(b)[Accredited in SA] - (for the record, I can't actually seem to find the text of this section anywhere). Thus, you should have no issues simply leaving the country (most countries require you leave for at least 24 hours) and then returning to get a new visa.
Please also note, that while you might legally be allowed to re-enter for another 90 days, an SA immigration officer could well question you about your past entry and why you are entering again so soon. Your visa exemption is also valid for most business purposed though, so you'll probably be alright.