1) Reboot the Computer. - Simple, I know... but it will fix so many "issues" without the need for any other steps to be taken.

2) Clean Your Caches - There are several tools that will do this for you, Onyx, MainMenu, Quicksilver...etc. Even if you don't have one of those you can still do it manually. Just delete everything in the folders Library/Caches and in Users/*Your User Name*/Library/Caches. When finished reboot.

3) Delete the .plist file - If it is a particular program that is giving you problems delete its preferences (.plist) in 'Your User Name'/Library/Preferences

4) Repair Disk Permissions - Go to Applications|Utilities|Disk Utility and select repair disk permissions on your OS X drive

5) Run Disk Repair - Boot from your restore/install disc and run a Volume/Disk repair on your startup disk.

6) Resetting the PRAM: When booting, hold down Command-Option-P-R and wait for the triple startup chimes.

7) File System Check - When booting up your computer hold down the Apple Key & the S key and it will boot into single user mode. When the text is done loading on the screen type in /sbin/fsck -f and hit enter. When that is done if it fixed things then do the check again to make sure it is cleared. When finished with that type in exit and it will start the computer in normal mode

8) Reset Nonvolatile Firmware - When booting, hold down Command-Option-O-F and wait for the command prompt. Type "reset-nvram" and hit enter.

9) Reinstall your OS: Insert the OSX disk and reboot holding down the "C" key. Install and archive your OS. You will not lose any of your settings or documents. Once the new install is complete test your Mac to see if the problem is gone. If the problem is gone than start adding the updates to OSX one by one. Make sure you check you Mac after each update to ensure it is working smoothly. Once you have reinstalled all updates and OSX use your mac for awhile and make sure it is operating like you would expect. After a while you can go into your folders and delete your old archived OS which does nothing but take up space.

10) If the problem persists than you need to do a erase and clean install. This will delete all you files, programs and settings so you need to back up these files. I also suggest that you back up your iLife files (iTunes, iPhoto, iWeb) files as well as your Application support folder in your Library folder. You might also want to save and export your bookmarks from you browser. This is a last measure because it is time consuming and resets your Mac to the way you received it but I do this at least once a year to clean out all the garbage that is left behind that can screw up your system. When you do this you want to be real careful about adding back third party software. I have found that as nice as some third party apps sound they are tested very well and often can play havoc with OSX, especially when Apple issues an update.