Thanks for the reply. It is helpful.
The first thing you need to understand is that assuming the original hard drive is in the machine, it is already more than 6 years old, and it is spins at a slow 5400 rpm rate. Any recommended disk maintenance/repairs might not result in much improvement, given what I stated earlier about the drive. Also, given that you do not have a more robust disk repair/maintenance program like Disk Warrior or TechTool Pro, you are relying on Disk Utility to "help you". Not sure if that is good enough, but that is what you are working with.
Additionally, I don't think the slowness is due to Apple's Mail program, as you indicted this happens both on start up, and when using an application like Safari (I'm assuming Mail is not running at any of those times).
So, to get started, you need to boot your Mac via the Recovery HD partition. What you need to do is press the Command and R keys as your machine is starting up. It will take some time, especially with your slow 5400 rpm drive, but eventually you'll get to the menu. One of those menu options is Disk Utility (I am not sure of the exact verbiage, as I use TechTool Pro (and once in a while Disk Warrior) for performing disk repairs/maintenance). Running Disk Utility in that environment is the best,as it is basically "isolated", and can do a better job with the repairs. What you need to do is 1) Verify and Repair the disk at the
Volume level, and 2) do a Verify and Repair Permissions, and a Verify and Repair disk at the
partition level. Hopefully, Disk Utility will give you some indication as to the "health" of your drive.
Assuming all that works fine, reboot your Mac normally. Note, however, that using Disk Utility to Verify and Repair permissions only does that for
Apple software. What you need to do next is to download and run the excellent free program called
Onyx. Besides repairing permissions for
any program, it also has some useful clean up functions. You can get Onyx from here:
http://www.macupdate.com/app/mac/11582/onyx
The other thing you should consider doing is defragmenting/optimizing the drive. That can be helpful to get it running faster and more smoothly. Unfortunately, I do not know of any freeware programs that can do this effectively. Such functions (Volume and File Optimizations) are included in TechTool Pro, and I have performed those tasks in the past for hard disks I have owned. The result was an improvement in speed. (I now have SSDs in both of my Macs, and only File Optimization is needed).
Finally, you might want to consider getting an SSD installed in your machine (you might be able to do it yourself). Your machine will feel like it got a breath of fresh air after installing one, as they are much, much faster than a standard hard drive.