Sorry, clicked on Send before the patch was attached.

With a gpg executable with default settings, org-encrypt-entry produces
output like this:

 -----BEGIN PGP MESSAGE-----
 Version: GnuPG v1.4.10 (GNU/Linux)

 jA0EAwMCBWZVym6QMPVgyTxreTb1AEL3uTO+qCh2lR9/Qxk4nEMpPr9/RwNk95Gb
 slUra9X+N+qSWghEHvvxY0Ol8Yw9Ko4n7JVhHFs=
 =E4vw
 -----END PGP MESSAGE-----

The first line (Version:...) can change from machine to machine and over
time (as gpg is updated with a new version.) This is problematic when
the file is stored under version control, because as you decrypt and
encrypt an entry that line will change and create differences among the
file on the workspace and the file stored on VC.

Second, the empty line just wastes space and it is plain ugly once we
remove the first one with the Version text.

Finally, on some systems (mostly Windows) depending on how your Emacs
and gpg are configured, ^M characters may appear at the end of every
line of gpg output once it is inserted on the Emacs buffer. This happens
when the buffer uses Unix line-endings but gpg uses DOS line-endings.

The patch removes all that junk from the encrypted text just before it
is inserted on the buffer.

I'm assuming that the transformations made by this patch are
uncontroversial and desirable. If anyone actually prefers to keep that
noise on his encrypted org entries, an alternative implementation that
uses a configurable list of regexps is trivial to implement, but then
every user would have to do some job for achieving the same result.