For video conferencing, I'd strongly suggest a commercial system that is guaranteed to work. I.e. one with a support contract.
If you wanna write a nice web front end to it, that would be fine, but I agree with Vincent that writing an entire video conferencing app in either Java or PHP is probably heading down a long road.
Better to try and use some pre-built tools for the heavy lifting. Real server is pretty nice, and I think there's a couple of open source collaboration stuff out there.
If you don't HAVE to use stored procedures, then you can make your application database neutral by using ODBC to connect to it.
As for Java versus PHP, I tend towards using PHP as the front end display logic language, and a database with constraints, triggers, stored procedures, and other tricks for stuff that has to have business rules. I.e. it's better to put your logic in the database, as non-transportable as that may be, since it provides the best performance metrics on reasonable hardware, compared to putting business logic into applets that run in a distributed web app environment like Java is used for.
I agree with vincent that Java tends to produce code with a large footprint that doesn't scale all that well.
The interesting thing about footprint is that I have seen things with large footprints scale moderately well. Cold Fusion under Linux springs to mind. It doesn't scale to hundreds of simo connections, but it can handle dozens quite well, but it's got a huge foot print. Luckily, it's fast enough that it can swap around all the work it has between 5 or 10 big fat threads and still run well.
Apache 1.3 is a multi-process design, whereby a single process is required for each connection. This demands lighter weight processes, which apache / php do quite well.
Java seems to use a lot of memory and provide near PHP speed nowadays. It's not bad, it's pretty fast, but I can't find a JVM that doesn't knock over dead at least once a month or so for no apparent reason. It's still running, but no longer serving pages. Not sure why, but Sun's and IBM's JVM both do it in my slight out of date tomcat (circa 6 months ago.)
Adding modules to PHP can be painful for the uninitiated or junior sysadmin, but once you've built it a few times, it's no big deal to add a module, even to a running box.
PHP's modules, however, integrate seemlessly with the environment. No include files, no compiler directives, no anything, just call the functions for whatever modules are there.
While Java has a large selection of modular code ready to be added, it too is a pain in the but to add to and configure, just in a different way.
But I would say the real choice is between Perl and PHP. Perl has the much MUCH larger code base available, is VERY fast with MOD_PERL or equivalent and is a solid reliable language.
The more important factor is that both PHP and Perl are Open Source languages. You don't like what's happening? Change it yourself. Java (the compiler/interpreter) is not Open Source or Free. I don't trust Sun anymore than Microsoft, and they seem to be holding Java a little too close to their chests for my comfort. I'd be happier if Java was implemented in a more open manner than it is right now. Given the Artistic license of Perl and the GPL/Zend licensing of PHP I know I can always fix problems if I really have to.