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Introduction to Linux - A Hands on Guide
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Have a look at Drupal.org, you can have a forum and blog up in no-time, then take a look at what other people already have done with it. Should give you some inspiration and if that's not enough you can always help with bugfixing.
This isn't really a Linux question (and not a lot Apache either).
For a working webapp I don't recommend re-inventing the wheel again, you're better of using a existing basic application and expanding it to your own desires (Drupal for example handles a lot already like security and pagebuilding, there are many other base systems available).
If you just need to prove you can build a site with PHP & MySQL then the options mentioned by Wim Sturkenboom above will keep you entertained for awhile, same goes for a forum or mailserver. You should be able to find plenty code samples on the net to get you started.
The usual very basic example is a system to track your CDs/DVDs/Books (whichever).
Store eg author/title/publisher (books) in DB tables, then write GUI forms in PHP to manage additions/deletions/updates & serve via Apache :-)