I'm assuming that you are running Mac OS X since you didn't specify it but the symptoms you are having suggest it (next time, please specify what Mac OS version you are using).
Try booting into Single User mode by holding down Apple-S after you hear the startup chime. This will drop you into a command line. Once at the prompt, type "/sbin/fsck -yf". This will cause the Mac to check the hard drive for any errors that might exist. Once it finishes, type "reboot" and your Macintosh should restart. HOpefully this will help any issues you might have.