The IRS's LMSB division has published guidance on substantiation of R&D costs that provides one more bit of support for NOT extending the credit, which provides a dollar for dollar reduction of tax liabilities, rather than the legitimate deduction or capitalization rules that would otherwise apply.
Research Credit Claims Audit Technique Guide, LMSB-04-0508-030 (May 30, 2008) responds to what has been seen in audits--a number of companies relying on "prepackaged RC Claim studies" that provide a lot of statistical analysis but don't actually prove that the expense (such as wages) is really connected to the research activity. Jack Cummings describes these studies as "obfuscating your lack of documentation by highlighting your mountain of unsupported data. This situation often results from putting together studies from a mathematical viewpoint, as contrasted with a legal/factual viewpoint. " Cummings Corporate Tax Insights, Checkpoint, 081208 (available to subscribers as preview).
Congress seems to think it "has to" enact extender legislation. Personally, I'd prefer to let most of these extender provisions just disappear. The R&D credit is a good candidate.