HP may be having a tough time of it right now, what with dismal earnings and an accounting scandal related to its $11 billion purchase of Autonomy, but one thing it doesn't have a problem with is R&D. For the first time in 3 years, Hewlett-Packard Co. (NYSE:HPQ) passed Intel Corp. (NASDAQ:INTC) for the most patents awarded in the Silicon Valley, earning 1,437 patents to Intel's 1,216. Read this week's paper to learn how other companies on the full Top 25 list fared this year. Then click on the slideshow…