I would would be wary of trying to develop an entire new Wiki-style
system unless there are significant reasons why none of the existing
packages would fit the needs we're envisioning. The investment of
time would be considerable, just to get a basic system up and running,
and time spent coding a Wiki is generally time not spent adding
content to it.
I would recommend instead installing something like MediaWiki or Twiki
and 'test driving' it for a while yourself, and seeing if it can be
made to serve your needs. Most of the more mature Wiki systems can be
installed to a point where they are up and running quite quickly, and
can then be customized with templates to make the UI simpler or to
help organize the site. With open source packages, the code itself
can be modified to solve problems or improve performance, and they
usually integrate quite well with other systems- in the past, we've
used Perl scripts or Unix shell scripts to automatically update
documents with new data to make sure that information is kept current
(for instance, it is possible to write a fairly simple program to
check all of the links on a page and 'prune' or flag any that are no
longer working).
Personally, I've used mySQL in the past in a variety of capacities.
Likewise with Perl. I've never had occasion to learn PHP, but I know
that a lot of popular web software uses it. PHP is a bit more focused
on web applications (and so a little easier for those purposes), while
Perl is a more general scripting langauge (but can be quite cryptic
and complex). I would say that it is more helpful to focus on the
features and ease of use of the existing packages, rather than their
implimentation, unless there is a particular reason that a certain
language can or can't be used (some hosting providers support Perl but
not PHP, or vice versa).