Many patent applicants have expressed some concern regarding the potential federal government shutdown after Friday, April 8th. The basic problem is that a federal agency is not supposed to spend any money without congressional authority to spend the money. This limit comes directly from the US Constitution, which says "No Money shall be drawn from the Treasury, but in Consequence of Appropriations made by Law." Article I, Section 9. That said, it is generally thought that essential federal employees can continue to work. For the most part, however, USPTO employees would not qualify as "essential."
Although the USPTO is fully user-fee funded, the agency still sends its revenue the Treasury and then draws money from the Treasury when needed. Thus, the USPTO will clearly be affected by the shutdown.
I contacted USPTO leaders regarding their contingency plain. The Office has crafted a short-term solution based on the fact that a portion of their monies-in-hand are not linked to the current fiscal year budget. Therefore, the lack of appropriations for the rest of FY2011 does not limit the USPTO's right and ability to spend that money. The Office's projection is that this funding source can take the agency through six business days. If the shutdown occurs at COB Friday, then the office would have funds through Monday, April 18. After that, the Office intends to continue to accept new application electronically.
The Office does not intend to offer any grace period for applicant deadlines missed during the shutdown.
Update: Press Release