It sounds like you need to do some house cleaning
Over time log files and other temp files build up every time you run an app or just boot the system. There are a few cleaners out there that can help you here. While you are at it delete anything that is just taking space needlessly.
This one is a little bit hard as you need to boot up under a different drive. This can be a USB thumb drive a USB or FireWire connected Hard Drive (some models won't boot under USB) or a CD/DVD that you have: Grey recovery disk or retail version of OS-X or one you have created. Once you have booted under the other drive you can then run Disk Utility from it to repair your internal drive. I do recommend making a backup copy of your files onto an external drive first just in case the drive fails.
The next issue is disk fragmentation. While people swear modern OS don't fragment this is a half truth. The issue is not the OS but filed you add and modify often frag. To resolve this you need a de-fragmentation tool. I personally like Drive Genius. there are others out there that will also work. I like zip in my system so I tend to run it twice a year (I work with quite a few files). Some people only need to do it once a year.
While you're at it you might want to think about cleaning out the dust build up internally. This will require opening your system as you didn't give details on it you'll need to post a new Question for us to cover that.
Basically, its just like owning a car, you do need to tend its maintenance needs so it runs smoothly and can give you a long life.