Please try using this CVS snapshot:

  http://snaps.php.net/php4-STABLE-latest.tar.gz
 
For Windows:
 
  http://snaps.php.net/win32/php4-win32-STABLE-latest.zip

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I am experiencing this same issue on SuSE 9.1 with PHP 4.3.4 and OpenSSH 3.8. This is a more recent PHP than the one you offered up to solve the problem.

I have narrowed it down to exec'ing ssh specifically. I am using passwordless public/private key authentication to a user account with very limited priveledges on the remote host.

The ssh command to the remote host is actually executed, but PHP never comes back.

The problem occurs using system(),shell_exec(), and popen().

I have reproduced this with a script as simple as:

<?php
system("ssh user@host mycommand_with_no_output");
?>
HTML GOES HERE


The result is that PHP never comes back, and it does not error out either.  Executing this via the command line works fine, executing it as a web-script hangs permanently.

One more note here- 
  I'm aware that there is a PECL extension to add ssh functionality to PHP. I would much prefer NOT to use that extension as it is dependant on a 3rd party library, not actual openssh code, so utilizing this library would create a dependancy on something my vendor does not support or provide bug/security fixes for. I'd much prefer to utilize what exists on the system.

scp is non-interactive, so it works fine in batch mode like that.  ssh is interactive and as such requires a controlling tty.  So it would likely work from PHP running in a TTY in CLI mode, but not from Apache since there is no underlying tty for ssh to attach to.  This is in no way a PHP bug.