They've "deprecated" tons of functions:
Security-Enhanced Versions of CRT Functions
I don't think everything on the list will bring up a deprecated warning (e.g. I don't think I've ever been warned off using printf) - but quite a few do. I don't think "deprecated" was the right choice of warning - since they apparently have no plans to remove support for them, and they're merely encouraging us to use the security enhanced ones.
Looking at the changes they've made in their *_s versions of the functions, they seem sensible and probably useful. That said, I'd personally ignore the warnings and the new functions -- I don't want to get into habits of coding that only work on one platform. If I
was only working on Windows with MSVC I'd consider using them.
I was interested to see that one of these changes is in C11 -- C11 removes the infamous gets(buf) and replaces it with gets_s(buf, len). Bout time!