Notice that some programs are not consistent in the way they insert the line breaks so you end up with some lines that have both a carrage return and a ^M and some lines that have a ^M and no carrage return (and so blend into one). There are two steps to clean this up.

1. replace all extraneous ^M:

:%s/^M$//g

BE SURE YOU MAKE the ^M USING "CTRL-V CTRL-M" NOT BY TYPING "CARROT M"! This expression will replace all the ^M's that have carriage returns after them with nothing. (The dollar ties the search to the end of a line)

2. replace all ^M's that need to have carriage returns:

:%s/^M/ /g

Once again: BE SURE YOU MAKE the ^M USING "CTRL-V CTRL-M" NOT BY TYPING "CARROT M"! This expression will replace all the ^M's that didn't have carriage returns after them with a carriage return.