Patently-O has a great post on the current numbers from the PTO.
Original patent application filings are down about 10% for the current fiscal year, while continuation filings are down about 20%. Continuation filings were particularly high in early FY2008 in anticipation of the new PTO rules that would limit continuation filings in the future.
The post is also interesting in that it tracks the PTO statistics on continuation and RCE filings. The PTO tracks Requests for Continued Examination (RCEs) as new application filings. Thus far in FY2009, 27.6% of patent application filings have been RCEs. This is up from 24.1% last year and 10-11% in FY2000-2002 (these numbers also include other forms of re-filing an application such as CPAs). Perhaps these numbers account for the rumored increase in the RCE filing fee.
The reasons for these numbers are not exactly clear, but one can certainly speculate. The economic downturn, the recent court decisions limiting patent rights, and the prospect of patent reform constitute a few reasons for the reduction in filings. The increase in RCE filings probably result from the decreased allowance rate, among other reasons.