The patentsystem (or rather said, the way the patentsystem is raped today makes it) is not a good way to prevent proctect the inventor's invention.
It might be so that many of the software patents of today will has been granted even if the shouldn't have been. But the costs of fighting an invalid patent is huge, and probably no small firm can survive a legal battle with one the giants.
Some good examples can be find here:
http://www.eff.org/patent/ (american patents)
http://webshop.ffii.org/ (example of european patents in a webshop)
The most important thing that one should remeber about patents is that the intention of patents is that the if the society gains more of giving one person a
monopoly on his/hers idea, a patent should be granted, otherwise it shouldn't be granted. Since you normally don't want a monopoly in a free market, patents are an exception for a situation where both the inventor(s)
and the society gains on having a time limited monopoly.
And I can't see how the public and the society gains anything by having patents on "one click shopping", "streming video" or 683 patents on the ethernet plug.