[hawski]

Most programs either write a full file every time and replace the old file by a single move or append to an old file. Writting in the middle could happen in a program writting to some kind of archive or disk image. There is probably a whole group of programs that do this I'm not familiar with, but I'm pretty sure of my first sentence.

[jefftk]

I'm not completely confident (I tried looking in the source and it wasn't immediately obvious) but I think emacs does small in-place edits when you're working with very large files.

[formerly_proven]

sqlite, dbm and similars, various zip libraries and the file formats build on that