It's true that there can be millions of files on your hard drive.
So here is another way of looking at things. How much is your time worth? Are you willing to spend hours going through hundreds of files and determining if you need them or not? Are you willing to risk damaging your software setup and having to troubleshoot your Macintosh if you trash the wrong thing? (I hear from several people each year who have borked their hard drive irrevocably doing this.)
Here is another option. (I'm not saying that this is the best option, but it is one to consider.)
FireWire hard drives are now very reasonably priced. You can even get a huge 1 Terabyte FireWire drive for only about $100 these days. Get a FireWire drive that is at least as big as your internal drive, but bigger would be better.
Clone everything from your internal drive onto the external drive using:
Carbon Copy Cloner (free)
http://www.bombich.com/software/ccc.html
Make sure that everything cloned onto the external drive is good.
Do an erase and install of OS X on the internal drive.
Your internal drive will now be like new. When you boot from it, your Macintosh should also be as fast as it was when it was new. You can choose to store new data on your internal drive or your external drive.
Maxtor 750GB FireWire hard drive
$80
http://shop.seagate.com/store/sgateus/en_US/buy/productID.156625000