By their estimates, $13.9 billion of classified procurement and $11.3 billion of classfied R&D is Air Force (96.5% of black procurement and 79.9% of the total estimated black budget), and $0.5 billion of classified procurement and $3.7 of classfied R&D is allocated to other defense department agencies (like DARPA and the Defense intelligence agencies). No classified procurement is allocated to the Army or Navy, while there is $2.2 billion for Navy R&D, and $0.2 billion for Army R&D.
What sort of stuff is it likely to be?
Aviation Week reports the programs include...
...a growing ability to invade sensors, create false targets, take over networks, plant misleading information and mine computer data, even from manned or unmanned aircraft flying close to the emitter of interest. A new generation of stealth—that will be invulnerable to low- as well as high-frequency radar—is being developed.
A lot of money has gone into technologies to find, disarm, jam or preempt the construction, planting and detonation of improvised explosive devices. High-power microwave devices are being designed to disable electronics, erase or scramble computer memories, or shut down electrical activity in road vehicles, aircraft in flight or satellites in orbit.
Another source speculates:
The concentration of classified funding in the Air Force's budget is the result of two factors . . . . First, the Air Force acquisition budget contributes funds to a number of intelligence agencies, including the Central Intelligence Agency, National Security Agency and National Reconnaissance Office. Second, the Air Force is responsible for most command, control, communications and intelligence functions.
Jane's has a nice historical overview. The article speculated seven and a half years ago that:
One likely strategic goal of current SAPs is the pursuit of what one senior engineer calls "the next stealth" - breakthrough technologies that provide a significant military advantage. Examples could include high-speed technology - permitting reconnaissance and strike aircraft to cruise above M45 - and visual and acoustic stealth measures, which could re-open the airspace below 15,000ft (4,600m) to manned and unmanned aircraft.
The existence of high-supersonic aircraft projects has been inferred from sighting reports, the repeated, unexplained sonic booms over the US and elsewhere, the abrupt retirement of the SR-71 and from the focus of white-world programs, such as NASP and follow-on research efforts such as the USAF's HyTech program. The latter have consistently been aimed at gathering data on speeds in the true hypersonic realm - well above M6, where subsonic-combustion ramjets give way to supersonic-combustion ramjets (scramjets) - implying that speeds from M3 to M6 present no major unsolved challenges.
One researcher in high-speed technology has confirmed to IDR that he has seen what appear to be photographs of an unidentified high-speed aircraft, obtained by a US publication. In a recent sighting at Area 51, a group of observers claim to have seen a highly blended slender-delta aircraft which closely resembles the aircraft seen over the North Sea in August 1999. Visual stealth measures were part of the original Have Blue program, and one prototype was to have been fitted with a counter-illumination system to reduce its detectability against a brightly lit sky. However, both prototypes were lost before either could be fitted with such a system. More recent work has focused on electrochromic materials - flat panels which can change color or tint when subjected to an electrical charge - and Lockheed Martin Skunk Works is known to have co-operated with the DoE's Lawrence Berkeley Laboratory on such materials.
Speculation about high speed aircraft has continued (and was discussed critically at this blog within the past year). My guess would be that it isn't the program that is in the production phase right now, and indeed, might be something used as a cover to generate speculation and take attention away from the real programs being produced.
I'd place more stock on a footnote in a 2004 Congressional press release that "significant funding that is also included in the classified portion of the defense budget for Boeing-related work on programs such as the Future Imagery Architecture (FIA)." Raytheon also touted classified intelligence contracts in 2004 and in 2007. A Spring 2007 list of codenames can be found here. The abrupt cancellation of a B-52 based electronic warfare program without a replacement in 2005 is also notable and could signal a covert replacement.
Second generation stealth could be very expensive, as could new spy planes (or spy satellites) or large drones. The estimated Air Force classified procurement (meaning buying stuff to actually use) numbers are high enough for 7 B-2 bombers or 63 F-22s in a single year, for example. The numbers are big enough to suggest that the Air Force has, at least, one active production line spitting out a non-prototype black aircraft model, and quite possibly several.
My guess is that the Navy's classified budget includes a big national missile defense component, and that the Army's piece is mostly small drones and counter-IED measures.
The defense agencies part is hardest to guess.
UPDATE: Nix the large drone theory. The plan to fly robot aircraft off aircraft carriers (the X-47) is public and has been awarded in a public bid (projected finish date in the year 2013). Presumably, the Air Force's parallel program (the X-45) will also be public. Also, the fact that they are only this far along in drone development on the Navy side argues against the existence a far more sophisticated black drone program.