Thanks, the fix works. I fixed php.ini afterwards, and it still works. 
I must accidentally have used "&" from the php.ini-production 
example line for arg_separator.output years ago. Strange that it 
haven't given me trouble before.

Try this fix.  Seems that some PHP servers have arg_separator.output 
set to '&' for some reason.  Which IMHO is completely broken 
behavior - URL separators are defined as '&'.  '&' is nothing more 
than an escaped/encoded version of the URL separator used in certain 
contexts, but certainly not all.

Changes have been made in Git for this ticket:

Bug #9903: Fix for PHP servers with broken arg_separator.output strings

  1 files changed, 2 insertions(+), 1 deletions(-)
http://git.horde.org/horde-git/-/commit/23c60e65beca4850e4a8ef50bac035de353cd4c8

FWIW, this is exactly what I get, and I am not seeing a double encoding issue.

Adding Jan, since he wrote Horde_Url.

2011-04-15T12:35:00+02:00 DEBUG: Variable information:
string(202) 
"void(Horde.popup('%7B%22url%22%3A%22%5C%2Fhorde%5C%2Fimp%5C%2Fview.php%22%2C%22menu%22%3A1%2C%22params%22%3A%22actionID%3Dview_source%26amp%3Bid%3D0%26amp%3Buid%3D44725%26amp%3Bmailbox%3DINBOX%22%7D'));"

Backtrace:
1. IMP_Contents->linkViewJS() /var/www/secure/horde/imp/message.php:566
2. Horde::debug() /var/www/secure/horde/imp/lib/Contents.php:857

2011-04-15T12:35:00+02:00 DEBUG: Variable information:
object(Horde_Url)#372 (6) {
   ["url"]=>
   string(19) "/horde/imp/view.php"
   ["raw"]=>
   bool(false)
   ["parameters"]=>
   array(0) {
   }
   ["pathInfo"]=>
   NULL
   ["anchor"]=>
   string(0) ""
   ["toStringCallback"]=>
   NULL
}

Backtrace:
1. IMP_Contents->linkViewJS() /var/www/secure/horde/imp/message.php:566
2. Horde::debug() /var/www/secure/horde/imp/lib/Contents.php:858

Next step - Horde::debug(Horde::url('view.php')) on the same line as before.

2011-04-14T10:22:59+02:00 DEBUG: Variable information:
string(203) 
"void(Horde.popup('%7B%22url%22%3A%22%5C%2Fhorde%5C%2Fimp%5C%2Fview.php%22%2C%22menu%22%3A1%2C%22params%22%3A%22actionID%3Dview_source%26amp%3Bid%3D1%2$

Backtrace:
1. IMP_Contents->linkViewJS() /var/www/secure/horde/imp/message.php:566
2. Horde::debug() /var/www/secure/horde/imp/lib/Contents.php:857

That *is* an invalid string - '[...]view_source%26amp%3Bid[...]' 
should be '[...]view_source%3Bid[...]'.  But the problem is neither I 
(nor Jan) can reproduce - we both get the 2nd encoded version while 
you are getting the 1st encoded version.

In imp/lib/Contents.php, in the function linkViewJS(), can you put a 
Horde::debug($url) call in after the line that begins '$url = 
Horde::popupJs(...'

Horde::debug() documentation: http://wiki.horde.org/Doc/Dev/DebugH4

My guess is that your system is auto-appending some kind of parameters 
to all URLs that is not happening here, so the ampersand 
auto-detection is failing in Horde_Url.

Whoops, copied the wrong line:

<a 
onclick="void(Horde.popup('%7B%22url%22%3A%22%5C%2Fhorde%5C%2Fimp%5C%2Fview.php%22%2C%22menu%22%3A1%2C%22params%22%3A%22actionID%3Dview_source%26amp%3Bid%3D1%26amp%3Buid%3D44691%26amp%3Bmailbox%3DINBOX%22%7D'));" class="widget" accesskey="M"><span class="accessKey">M</span>essage 
Source</a>

Yes, the generated code looks like this:

<a 
href="javascript:void(Horde.popup('%7B%22url%22%3A%22%5C%2Fhorde%5C%2Fimp%5C%2Fcompose.php%22%2C%22params%22%3A%22actionID%3Dredirect_compose%26amp%3Bidentity%3D0%26amp%3Bthismailbox%3DINBOX%26amp%3Buid%3D44691%22%7D'));" class="widget" accesskey="t">Redirec<span 
class="accessKey">t</span></a>

which turns into this:

https://<site>/horde/imp/view.php?actionID=view_source&amp%3Bid=1&amp%3Buid=44691&amp%3Bmailbox=INBOX&uniq=1302724661776

and thus doesn't work. Can I give you some more details about my setup?

There is no link content, there is only onclick javascript content. 
And that works perfectly fine for me.

Traditional IMP interface (screenshot attached).

Using which interface?

I have just upgraded from Horde 3.3 to 4.0. I did a fresh install, 
reconfigured everything and let Horde upgrade the DB schemas.

The link "Message Source" when viewing a mail message is wrong in this 
version. Example of generated link:

https://site/horde/imp/view.php?actionID=view_source&amp%3Bid=1&amp%3Buid=44676&amp%3Bmailbox=INBOX&uniq=1302717323354

If I copy the URL and change it to:

https://site/horde/imp/view.php?actionID=view_source&id=1&uid=44676&mailbox=INBOX&uniq=1302717323354

it works. Tried with both Chrome, Firefox and IE.