Our general policy is to make Moodle standalone and independent of PEAR. PEAR has not been as reliable as you might think (eg not included on cheap web hosts etc).
Where we've used PEAR extensions we've included copies in Moodle core, and gone through some trouble to allow them to be licensed as GPL to make this legal:
http://docs.moodle.org/en/Credits
Most of the PEAR libraries are accessed by some other API in /lib, and sometimes these will go to the trouble of checking and using a real separate PEAR version if it exists, and only falling back to the included version if necessary. This is the preferred way to handle these things.
As asked here: http://moodle.org/mod/forum/discuss.php?d=98420 since moodle networking is the apparent direction of future development, is PEAR xmlrpc going to be addressed? Will someone identify whether there are or will be options here?