The one thing that I never saw make the leap from BeOS to other operating systems in a meaningful way was the "an application is a thin wrapper around a directory of metadata-enriched files" model that BeOS did.
I think the mail application and the media player were largely built this way because Be needed to build a handful of demonstration applications quickly and cheaply. On the other hand, I remember thinking how nice it was that email and multimedia behaved like the file browser with all its search and filtering features.
iTunes always felt like the exact antithesis of the BeOS model. It was a heavyweight application that had its own interaction model and idiosyncrasies. It might as well have been its own OS by comparison.
I think that's a legacy from MacOS Classic, where there was a way of keeping a handle to a file that was independent of the file's name (so you'd still point at the same file even if it was renamed).
You might find the file handle stuff comes from the fact that a lot of the Be employees were originally Mac developers at the start, and quite possibly because they wanted to support some of the features that were in the OFS (original File System, the Database like file system BeOS originally shipped with right up to the AA/PR1 releases. DR8.x definitely had the old file system.)
I remember reading some BeOS API documentation where it said something like "paths are UNIX-like, entry_refs are MacOS-like and they each have some pros and cons". Can't find it now, though…
