For epubs from the same source, epubcfi[1] can be used to point to a passage. It is somewhat resilient to editing, as long as the gross structure of the document remains the same. (Parent tags, file name, ids.) iBooks uses this standard for annotations, but doesn't expose it anywhere.[2] I don't know if any other book readers use epubcfi for annotations.
I think mobi files loose enough structure in translation that it wouldn't be possible to locate an epubcfi pointer within them. However, it might work with the newer "format 8" files, if they are converted from an epub. (I haven't investigated how much structure is lost.)
[2]: some records in my database don't have an epubcfi, but I haven't investigated whether they're user-created annotations or internal ones. (e.g. current location)
I think mobi files loose enough structure in translation that it wouldn't be possible to locate an epubcfi pointer within them. However, it might work with the newer "format 8" files, if they are converted from an epub. (I haven't investigated how much structure is lost.)
[1]: http://www.idpf.org/epub/linking/cfi/epub-cfi.html
[2]: some records in my database don't have an epubcfi, but I haven't investigated whether they're user-created annotations or internal ones. (e.g. current location)