There are some advantages to using the provided Apache installation
- It's there, no install required
- You can use the server admin tools to set up your sites
- It can be updated by Apple Updates
But for any serious use I would recommend installing your own...
- The server admin only goes so far, any normal amount of tweaking still needs to be done in the config files
- You have the choice of version 1.3, 2 or 2.2
- Apple are not particularly quick at updating Apache - if ever (same goes for MySQL PHP etc)
- The Apple admin console has been known to overwrite your changes to the config files
- If you are used to *NIX, Apple installs everything in weird places...
- Any big changes in configuration may break other Apple programs that rely on the provided Apache (Software update, Wiki Server...)
Going beyond the scope of your question - I would probably not recommend running Apache on OS X server at all - but if you have to, install your own.
My 10.6.0 Server has the following versions
- Apache 2.2.11
- MySQL 5.0.82
- PHP 5.3.0