Let it pass buddy, let it pass.
If you wanted to Patent your work, I hate to say it, but as the voice of total logic if you wanted your work patented you should have done it whenever you were finished writing your code.
On your own HeapCheck disclaimer page you say "I am releasing my humble efforts to the public so that some programmer's life gets a little easier."
You can't then file for a patent on that work, because you put it out and stated that you were releasing it to the public. Essentially you waived all exclusive rights to your work when you released it for free to the public. You can't suddenly decide that because IBM used it that you want to cash in. You said you released it to the public.
Now I know you have it under the GPL but if you state elsewhere on the same site that you're releasing your efforts to the public I'm pretty sure the courts are going to see that in very lenient terms for IBM. They have every right to think they are free to use it if you state that you are releasing it to the public. Your best bet, I would think would be to contact a patent attorney and run your case by them. Realistically given your statement that it's been released to the public the only grounds that I can see you challenging their patent on is that they aren't following the terms of the GPL. But the even with the restrictions placed by the GPL if the work IBM did is substantially new they'll still be able to patent their work. For example you say they are accomplishing the same goal, but if their means of execution are substantially different than yours then your patent doesn't apply. Additionally a patent lasts only 18 years, and you haven't brought any other previous claims, even when you found Microsoft to be doing the same thing IBM is now. That will hurt your case big time.
Ultimately though my advice isn't based on the law. I'm not a lawyer and I think when it comes to patent law NO ONE really knows what's going on because so much of it is just winging it. But I think most patent lawyers would probably tell you that legally it would be hard to pursue your case because you said you were releasing it to the public, you never issued a patent claim about anyone else using your work, it's not even clear (since we don't have the code) if IBM used your code or if they just liked what your code did and figured out a different way to accomplish the same goal. But ultimately all those things are irrelevant, because I'm pretty sure if you run this by most patent attorneys they'll probably tell you that suing IBM is virtually impossible. IBM made $2.6B the first quarter of 2010. IBM can and does afford the best, and I'm sure one of the most ridiculously abundant legal teams, of any company in the world. Talk to a patent attorney see what they tell you, but don't be surprised if it gets into the simple logistics of suing a company that has a regular cash flow of nearly $20B dollars per quarter.