Here’s the deal with GPL compatibility. I’m not a lawyer, but I am a Debian developer, and thus have been steeped in this stuff for years. And I’ve helped write free and GPL-compatible licenses. But for a definitive answer, hire your own lawyer. This isn’t legal advice, and I’ll remind the judge of that should you sue me because you took my advice and lost out. Not that you would, of course; you don’t look that gullible. 🙂
In the following, I’m going to assume that the PEAR license and the GPL are not compatible. I haven’t read them, though, so I can’t say for sure.
First of all, people who just use GPL software don’t have anything to worry about, period. They can use their GPL software with PEAR, OpenSSL, Oracle, Microsoft Word, whatever. (At least, that’s true from the perspective of the GPL; you’ll have to check the licenses of the other software to see what they allow, especially if the “license” is actually a contract that imposes restrictions beyond copyright.)
So what’s the problem? The problem comes up when people do things that invoke copyright law, such as modifying software, or creating new copies of software (outside of fair use), or distributing those copies to other people. When you do those things, you have to respect the copyright licenses on all of the items you’re modifying/distributing/whatever.
Now, the GPL says that you have to give all of the freedoms of the GPL to anyone you distribute to. So, if you add some code to the GPL software that, say, doesn’t allow commercial use, you aren’t allowed to distribute that modified software, because the GPL allows commercial use.
This is pretty cut and dried when it comes to software you must have to run other software. So, for example, if the PHP license were incompatible with the GPL, you couldn’t license PHP code with the GPL, period. (It isn’t incompatible, as far as I know, BTW.)
What’s fun is when you don’t absolutely need other software to work, but you can use other software if it’s present, like what you’re describing with PEAR. In that case, the GPL doesn’t allow you to distribute the two things together. But remember that rule for end-users: they can’t get in trouble (under the GPL) for combining, say, WPMU and PEAR, because they’re not doing anything that steps on anyone’s copyright by just using the code.
So, in summary, yes, your users should be OK.
Incidentally, you can modify your code in WPMU and add PEAR support all you want, because you’re the copyright holder. But if you’ve modified original WordPress code and added PEAR support, you might want to talk to Mark about it, because technically there’s a contradiction in the licenses, and Mark could sue you over it for violating his copyright. (I’m not implying he would; just making an observation about the law.)