Answer written by Jan Lehnardt, Tomas V.V. Cox and Rasmus Lerdorf.
Currently PEAR supports the following list of licenses:
PHP License
Apache License
LGPL
BSD style
Other licenses may be added to this list on a case-by-case basis. Please get in touch with the PEAR developers mailing list for this.
For PECL extensions that are linked into PHP, the license must be compatible with the PHP license. That means you can not GPL a PECL extension or you would be violating the GPL. Note also that if you write an extension that links against a GPL'ed library you will be violating the GPL. If you need to link against a GPL'ed library, get permission from the author of the library.
To set the license of you PEAR/PECL package, put it in the head of all source code files of your package and also the type of it inside the <license> tag of your package description file (package.xml).