There seems to be something inherently wrong with how PEAR is packaged in Debian/Ubuntu (hence referred to as Debian, since Ubuntu doesn't modify the php5 source package with regards to PEAR). A bit of background: I'm currently trying to update the PHPUnit package to the current version (the Debian version seems to be stuck at 3.2.x — 3.3.9 was released the day this was written). I'm (re-)running dh-make-php to accomplish this, mostly because there doesn't appear to be a very obvious way of upgrading PEAR packaging for Debian (given package.xml, etc.). The problem is that PEAR is bundled with PHP on Debian, courtesy of the php-pear package. The one on Ubuntu's Hardy Heron is stuck at 1.6.1, whereas the current version (again, as of the day this was written) is 1.7.2. I can't use dh-make-pear to package the latest PHPUnit because the package.xml file requires PEAR 1.7.1 to parse it.
Now, Ubuntu's community documentation for PEAR recommends upgrading PEAR via the pear command. That seems counterproductive to me. Given that pear, by default, installs to the same location as the package, I presume that PEAR and any other "pre-installed" package that was pear-upgraded would be reverted, in particular if there's a security release. This makes the sysadmin's job harder, obviously. I can't seem to find any rationale for this packaging behavior (admittedly, I didn't look very hard). But other distros get it right - Gentoo definitely packages the non-bundled PEAR versions, and from a cursory search, it appears that Fedora does as well.
So, what's my solution (for now)? Backport the latest stable PEAR into the php5 source package.