Change EOL on multiple files in one go
Solution 1:
The Replace dialog can handle extended characters like EOL. Just change "Search Mode" to "Extended", and you can work with EOL (\r\n in Windows or \n in Unix), tabs (\t), etc.
You can also use the Find in Files tab of the dialog to do the replace across multiple files.
Solution 2:
I have Notepad++ 6.1.2.
In "Edit" menu you have "EOL conversion" that does exactly what you need.