There should be a plugin (or a built-in option) to automatically save text files with CR/LF end of line-encodings if the file is to be saved to a Windows partition (FAT, NTFS). 

Rationale: if you're saving a text file on a Windows (or Mac) partition, you're likely to use it in a mixed operating system environment.

I know it's similar to bug 103753, but the important issue is that the plugin automatically chooses the correct encoding.