I was under the impression that the key one is the part of FAT/FAT32 that allowed files with long filenames and how those filenames can then be uniquely represented in a system that doesn't support them.
Basically a hideous hack job that resulted in all that "THISIS~1.TXT" in the distant past.
Interestingly this is the patent that was ruled invalid by the German courts at the end of 2013. I believe a document was found written by Linus Torvalds that predated the patent by 3 years. All the points in Microsofts patent that distinguished it from the Torvalds paper were found to not satisfy the technical requirements.
I assume it's still chugging along through a myriad of appeals.