Running PHP 5.2 and 5.3 on same apache server instance

Run one as an apache module and one as fast cgi and you'll be fine, you can even do this on a virtual host basis by assigning the file handlers in the virtual host.

However I've no idea if you can find packages for both version of php that will install along side each other, I imagine in most distros they will overwrite each other. You may have to compile yourself.

Another way to avoid compiling things yourself (I tend to try to avoid that at all costs as it makes keeping the system up to date a lot harder) is to run a separate system in a chroot jail:

https://help.ubuntu.com/community/BasicChroot

It's very easy to set up, and you can update both outside and inside the chroot jail just by using (twice, obviously) apt-get or aptitude. The downside is that it's kind of overkill, and you'll need a second IP to do it. The upside is that you can have different packages installed inside the chroot jail.