PECL versioning has historically been fairly anarchic. This made it impossible to determine the status of an extension, or whether an update would break binary compatibility with previous versions (or work with a given PHP release) without a long try-&-fail process. Some of the processes in php.net that currently use hard-coded lists could also benefit from a standardized versioning process.
The base proposal was implemented across PECL by April 2008. Only the question of what to do about PHP extensions that are both in PECL and in the PHP core - and usually symlinked - remains open. It would be nice to resolve this before the PHP 5.3.0 release!
There are actually two RFCs (proposals) to deal with version numbering in PECL and for core PHP extensions in general.