Department of Defense (DOD) R&D in the omnibus appropriations package is really two stories in one. According to AAAS estimates, overall DOD R&D will come down by $8.4 billion, or 11.2 percent, below FY 2012 levels, and will even fall below FY 2013 post-sequestration estimates by nearly $2 billion, or 2.9 percent. But not all programs will bear the burden of these cuts equally. The decline is entirely driven by cuts to the Department's downstream technology development accounts (dubbed "6.4" to "6.7" in the DOD nomenclature). These accounts are focused on transitioning technology systems from the lab to the operating environment in advance of procurement, and on development and engineering support for maturing or already-fielded weapons systems, vehicles, and communications platforms. Funding recipients are primarily defense contractors. For instance, DOD's $460 million R&D budget for the F-22 Raptor aircraft, which has been operational for some years, appears in these accounts. Collectively, they will drop by 4.2 percent below FY 2013 levels under the appropriation.
On the other side of the coin are the science and technology programs, including activities in accounts 6.1 to 6.3 and DOD's extramural medical research program. These programs will collectively increase by 8.1 percent above FY 2013 levels, keep pace with inflation relative to FY 2012, and top the President's request. The clearest winner here is medical research, which received twice what the Administration had requested, but basic research also receive a boost. Applied research and advanced technology development, the other two S&T accounts, were also increased, but will remain below FY 2012 funding levels after inflation.
The below chart lists the basic breakdown for DOD R&D by account; also see this summary chart  by military departments (including DARPA).
The sharp decline in the development and engineering accounts, and the relative health of the science and technology accounts, matches recent history. All classes of DOD R&D increased rapidly following September 11 and remained elevated before declining, but the swings up and down have been more moderate for the S&T programs than for the larger downstream accounts.