Simple. When it shows up in the Software Update list, hit the backspace key, or in one of the menu items there will be an option to ignore the update, which means it won't show up in your list again until there's a new version.
Since upgrading HP drivers for my printer from the HP web site, HP Printer Software Update 2.8 keeps showing up from Apple. I install it, it shows up as having installed correctly, then it shows up in Software Update again, even after rebooting. I suppose I can ignore it indefinitely, but that will get old.