I have a webpage setup with PHP, Apache and MySQL.
Lately, the process mysqld-nt.exe is almost always using the 50% of the CPU (I guess consuming one of the two cores), and the Database performance overall is quite slow.

And sometimes, a quite big query is executing and only the 50% of the CPU is being used and I think that it should use all the available resources to make the querys faster.

Is there anything I can do to improve this situation?

I tried to "Optimize" all the DB, and "Repair" some of the tables that are quite big.

You're just going to have to learn how to use SQL better and fix your queries. If you want good targeted help, you'll need to explain the layout of the database and show us your sql queries and stored procedures. One of the best places to start is the optimization chapter in MySQL's manual; beyond that you'll need a good book on SQL, database design, optimization, and integration. You will likely need to change your PHP to use the database better - most PHP sites are pretty naively coded.

Things you can do without the mental effort:
Update mysql to 5.0 or 5.1.
Update to the alpha 6.0 for multithreading (but beware of alpha crashes!).
Upgrade your CPU to a core2.
Switch to a faster database engine, like postgresql, which is long since multithreaded.

-foxyshadis