Use sed to add a newline to the end of a file (this will perform an in-place replacement and create a backup file, MYFILE.bak):

$ sed -i.bak '$G' MYFILE

Some programs, such as Emacs, will omit the trailing newline from a file unless configured to add one. Emacs can be configured to add a newline automatically.

There are a few different ways to convert a DOS file to Unix format, but the most available is probably this:

$ col -bx < dosfile > unixfile

Given an array @slobber, replace all the CR-LF with CR:

foreach (@slobber) {
   s/\015\012$/\n/; print;
}