Recipe from "emacs -Q":
1. Download the two attached files `fa' and `fb'.
2. M-x diff RET fb RET fa RET

In the *Diff* buffer, I see annoying/inappropriate "^M" characters at
the end of the compared lines. (see attached screenshot)

I see this bug both in the emacs-24 branch and the trunk.

In GNU Emacs 24.2.93.1 (i386-mingw-nt6.1.7601)
 of 2013-02-10 on VBOX-W7
Bzr revision: 111243 michael.albinus@gmx.de-20130210100709-s22fi7zl9w92a8sa
Windowing system distributor `Microsoft Corp.', version 6.1.7601
Configured using:
 `configure --with-gcc (4.7) --no-opt --enable-checking --cflags
 -IC:/emacs/libs/libXpm-3.5.10/include -IC:/emacs/libs/libXpm-3.5.10/src
 -IC:/emacs/libs/libpng-dev_1.4.3-1_win32/include
 -IC:/emacs/libs/zlib-dev_1.2.5-2_win32/include
 -IC:/emacs/libs/giflib-4.1.4-1-lib/include
 -IC:/emacs/libs/jpeg-6b-4-lib/include
 -IC:/emacs/libs/tiff-3.8.2-1-lib/include
 -IC:/emacs/libs/libxml2-2.7.8-w32-bin/include/libxml2
 -IC:/emacs/libs/gnutls-3.1.5-w32/include
 -IC:/emacs/libs/libiconv-1.14-2-mingw32-dev/include'


-- 
Dani Moncayo