IANAL, but I think many patent lawyers would suggest that Bob consider a provisional patent application. This generally much cheaper to draft and file than a full patent application, it gives you an earlier filing date if you decide to go for a full patent, and makes your invention more likely to show up in a prior art search. You'll still have to invest time, and $2,000-$3,000 dollars, but it will probably give Bob some extra protection against someone else patenting his software.

http://inventors.about.com/od/provisionalpatent/a/Provisiona...

http://www.ipwatchdog.com/patent/provisional-patents/

There's nothing you can do to prevent someone coming after you. You can only protect yourself if you plan to have the means to actually fight the case. This is one of those areas where an accusation and intent to pursue a fight from a "big dog" can be bad enough to crush the "little guy".

Sorry, my point was whether or not Bob should go file for a patent himself.

I get why people call software patents evil, but they seem kind of necessary to protect against bigger companies (at least until the patent system is 'fixed').

Sure, go for the patent.

The problem is litigating the twenty or so patents any large company can pull out of the bag, which, if you squint at the blurry lines, might overlap with what you are working on.

Basically, yes, having a patent yourself would be a great help, but it doesn't solve the problem when people are getting patents on what amounts to standard practice.

Yea, in this case I am suggesting that he shouldn't go file for a patent himself. It is expensive, a distraction, and offers no meaningful protection against deep-pockets.