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First off, almost all MTAs and forwarding agents will prepend a Received: header noting the handover details (date of reception, hostname of receiving MTA, HELO name of sending agent, and IP address and possibly rDNS of sending agent).

Please be sure to note if the header is prepended, appended, or if header order and formatting is maintained for existing headers.

Mailing List Managers

Mailman, appends the headers List-Id, List-Owner, List-Post, List-Subscribe, List-Unsubscribe, List-Help, Precedence, Sender, and Reply-To, by default.

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LYRIS list software will move Message-Id to X-Message-Id and create a new Message-Id. It's unclear what other headers are added or modifications are made.

Yahoo! Groups adds X-Originating-Ip, X-Yahoo-Profile, Mailing-List, Delivered-To, Precedence, List-Unsubscribe, X-Sender, X-Apparently-To and sometimes X-Egroups-From. Some headers are appended, some are prepended.

Relays

MS Exchange will reformat From, To, Received, and Message-Id headers, and may remove headers and even entire MIME parts, depending on its configuration.

Sendmail may convert character sets during message reception (noted on 8.11.6). This results in appending a X-MIME-Autoconverted header noting the details:

X-MIME-Autoconverted: from quoted-printable to 8bit by dogma.slashnull.org id h33M4ac02828

Almost all MTAs will add Date and Message-Id headers if not already present, and will qualify unqualified addresses (no hostname) in the From, To and CC headers.

Filters

SpamAssassin adds the headers X-Spam-Status, X-Spam-Level, X-Spam-Checker-Version and (conditionally) X-Spam-Flag; SA 2.6x allows complex control over what headers can be added.

MUAs

Evolution appends the header X-Evolution.

Eudora adds the following tags to HTML MIME parts: <x-html>, <x-stuff-for-pete>.

MH prepends the headers Replied, Forwarded, and some others.