The papers are from JSTOR, not MIT. MIT pays for a subscription to JSTOR like many other universities do.
1) DSpace http://dspace.mit.edu (an open publishing platform for academic material. Most all theses produced by MIT researchers can be accessed by the public here)
2) as an MIT technical report (mostly published via dspace)
3) as an MIT "Working Paper"
You can find more information here: http://libraries.mit.edu/docs/research-publications.html
Certainly, a huge number of MIT publications do end up being mirrored in JSTOR, but they are usually published via whatever journal or conference proceeding they are accepted to first. If an author cannot find a journal that is willing to publish their paper, then they will probably issue it as an MIT technical report.