TYPO3 Core

Check this with the current test version at http://www.jambage.com/index.php?id=170 ,

open typo3conf/ext/sr_feuser_register/lib/class.tx_srfeuserregister_email.php
and find the line where is

$Typo3_htmlmail->addPlain(str_replace("[","--",$PLAINContent));

and just above it add the following lines:

$PLAINContent = str_replace("[","--",$PLAINContent);
$PLAINContent = str_replace("]","++",$PLAINContent);

then go to index.php and find these lines:

// **********
// Constants defined
// **********

and under that, write these lines:

if ($_GET["tx_srfeuserregister_pi1--sFK__"]=="APPROVE") {
$url_self = str_replace("++","]",$_SERVER["REQUEST_URI"]);
$url_self = str_replace("--","[",$url_self);

//echo $url_self;
    header("location: $url_self");
}

it's not the best, but it works for me. i hope this helps.

You are replacing the '[' and ']' in the generated urls. This could help to get all confirmation links in every email client working. However this should not be fixed in this extension but generally in TYPO3. So make a feature request to this on the TYPO3 Core bug tracker.

Have a look at RFC 2396 on "URI generic syntax" ( http://www.ietf.org/rfc/rfc2396.txt ):

-------SNIP-------
2.4.3. Excluded US-ASCII Characters

Although they are disallowed within the URI syntax, we include here a
   description of those US-ASCII characters that have been excluded and
   the reasons for their exclusion.

The control characters in the US-ASCII coded character set are not
   used within a URI, both because they are non-printable and because
   they are likely to be misinterpreted by some control mechanisms.

control     = <US-ASCII coded characters 00-1F and 7F hexadecimal>

The space character is excluded because significant spaces may
   disappear and insignificant spaces may be introduced when URI are
   transcribed or typeset or subjected to the treatment of word-
   processing programs.  Whitespace is also used to delimit URI in many
   contexts.

space       = <US-ASCII coded character 20 hexadecimal>

The angle-bracket "<" and ">" and double-quote (") characters are
   excluded because they are often used as the delimiters around URI in
   text documents and protocol fields.  The character "#" is excluded
   because it is used to delimit a URI from a fragment identifier in URI
   references (Section 4). The percent character "%" is excluded because
   it is used for the encoding of escaped characters.

delims      = "<" | ">" | "#" | "%" | <">

Other characters are excluded because gateways and other transport
   agents are known to sometimes modify such characters, or they are
   used as delimiters.

unwise      = "{" | "}" | "|" | "\" | "^" | "[" | "]" | "`"

Data corresponding to excluded characters must be escaped in order to
   be properly represented within a URI.
-------SNAP-------

The bottomline is that this is NOT a mail client bug but that the URLs in TYPO3 confirmation emails should be changed. The square brackets should be escaped to %5B and %5D.
For some mail clients (like Apple mail app) it also works to enclose the URLs in quotes or angle brackets (as Gregor proposed in his original report). Both delimiters result in correct links in Thunderbird and other email clients (like Apple mail app).
But IMHO the way to go is escaping as the RFC recommends.