I've now got PEAR to work on SME Server 6.0.1-1. Simple, once I worked it out, but not initially obvious to me at all.
PHP is always limited to using 'include' and 'require' scripts located in or below the directory specified in the PHP directive set in 'open_basedir'. By default on SME Server this is the Primary ibay (/home/e-smith/files/ibays/Primary).
PEAR scripts in the default installation directory are in /usr/share/pear which is OUTSIDE the base directory tree, and hence 'includes' of PEAR modules just don't work, but don't give an error, either.
I found this out the hard way, by remembering I had had this problem before, when trying to put certain 'confidential' php scripts outside the web server document root (...Primary/html on SME Server), and finding that they had to stay within the Primary directory tree. I reinstalled the PEAR modules, choosing to put the scripts in Primary/share/ and subdirectories, then having the install script add this directory tree to the PHP include_path in php.ini.
I can now see (I think, but haven't yet tried) that it should also work if I leave the PEAR install in the default /usr/share/pear, and instead of relocation all the scripts, I just add a second path of /usr/share/pear to the open_basedir directive in php.ini (and then to the custom template that changes php.ini on a reboot, so I don't lose it).
But WHY, oh WHY, can't the otherwise excellent install scripts for PEAR, and/or the SME Server setups do this for us? I've wasted literally a day working this out for myself, and either no one else using SME Server uses PEAR (improbable) or everyone else is a clever enough LAMP (Linux, Apache, MySQL and PHP) guru just to 'know' the answer!
If there is anyone else stuck in the same position, maybe this will save them some time.
John McC