I would like to wipe my entire hard drive and reinstall Lion from scratch. I try to use the Lion Recovery tool but it does not wipe the disk so I still have all my installed programs that I don't want. I do not want to delete them by hand just want to do a clean install of the OS.
I just did this yesterday, so it's still fresh in my mind. Make sure that when you restart your computer, you hold Cmd-R to enter recovery mode. Inside that, choose "Disk Utility" and there you can erase your Mac OSX partition.
If you do not do that and simply select "Reinstall Mac OS X", then it will not erase your drive, but just overwrite the parts that need to be overwritten.
Note that you will not be able to erase the Lion recovery partition this way. All options to modify this partition are disabled in Disk Utility. There is really no need to wipe this, and erasing and formatting the main partition should be sufficient.
Download and run the Lion Recovery Disk Assistant. This will let you put a bootable Lion installer on a USB stick. Then reboot, holding option, and select the USB drive you just created. You will then be able to completely wipe and repartition your internal drive and reinstall Lion.
Check out this other Q:A, which details many ways of installing Lion, including creating media so that you can perform a clean install from a DVD, without needing to use the restore partition.