This may not be useful for answering the "hacked a (non-computer) system" question on the YC application form, but I think a script which can run on a linux system and construct a bootable FreeBSD image qualifies as a cool hack nonetheless.
Not particularly, but I love the idea. The depenguinator isn't really about making people switch from linux to FreeBSD; rather, it's about allowing people to install FreeBSD where they otherwise would not be able to -- most commonly, on servers rented from cheap dedicated server hosting companies which support linux but don't support FreeBSD.
Some linux distributions disabled hyperthreading by default as I recommended; others didn't. Some cryptographic libraries have fixed some of the more obvious ways that this can be exploited, but no library is completely immune. Intel hasn't done useful at all.