There is a chance I suppose you've been "rooted". Things you can do to find out -
See if there is a .rhosts file created in your /root directory with a "+ +" entry. This is a bad sign.
Have a look in your /etc/passwd and /etc/shadow files for strange logons.
Download, install and run a "check rootkit".
Think about using some sort of intrusion detection, like tripwire or snort in future.
Do a "netstat -pln" and suss out the processes that are listening.
Check the security section of these forums, do some searches. If you've been hacked and it's causing a slowdown the hacker must be using your box for something and it won't be hard finding out what that is.
Check your space too, maybe you have huge logs that are pinching space and making fragmentation. Anyway, best of luck with your server and post the result when you get to the bottom of things