I have created a branch that set the line endings of files to be managed through Git. (line-endings)
To make sure your line endings are ok, after pulling from it, merging and commiting, delete ALL the files in the working directory (except files under the git directory .git) and do git reset --hard
From then on, you never have to worry about line endings and huge whitespace changes any more.
This is based on the current SupSupr's master, so you may have many merge conflicts if you have moved a long way from it. But just taking the .gitattributes file from it should help normalize your line endings.