Adobe InDesign, for one. I don't know about the current version, but version 2.0 has a non-standard print dialog box which does not include the print to PDF option, among others. I believe this approach is common with Adobe applications, or at least it was.
Since OS support for printing to PDF started with OSX, I don't know that length of Mac use is really an issue here, but if it matters, I've been a Mac user since 1984, and over the years I've seen quite a few applications which monkey with the core services of the OS, such as printing.
Well, let's not count Adobe's applications (actually I've always known about this) as they generally ship with the Adobe Reader application which allows for saving as PDF. Remember Adobe is most known by even novice users for their PDF reader. It makes sense that they would create their software to work along side with Reader.
I'm just happy that Preview is so advanced now that I don't have to be slave to using that bloated Adobe Reader anymore.