The kind of model I prefer is something based on atomicity. Most applications can get by with file-level atomicity--make whole file read/writes atomic with a copy-on-write model, and you can eliminate whole classes of filesystem bugs pretty quickly. (Note that something like writeFileAtomic is already a common primitive in many high-level filesystem APIs, and it's something that's already easily buildable with regular POSIX APIs). For cases like logging, you can extend the model slightly with atomic appends, where the only kind of write allowed is to atomically append a chunk of data to the file (so readers can only possibly either see no new data or the entire chunk of data at once).

I'm less knowledgeable about the way DBs interact with the filesystem, but there the solution is probably ditching the concept of the file stream entirely and just treating files as a sparse map of offsets to blocks, which can be atomically updated. (My understanding is that DBs basically do this already, except that "atomically updated" is difficult with the current APIs).