Underfunding of basic research. The federal budget for R&D in 2006 (the last year that Republicans held a majority in the Congress) was $132.3 billion. In constant FY 2005 dollars (used hereafter), this broke down to around $73 billion in defense related R&D and $56 billion in non-defense R&D.
Defense R&D increased 2001-2006 from $50 billion to $73 billion. Most of this increase came from weapons development, not basic science. From 2001-2005, defense spending on science and technology (basic research) rose from slightly more than $10 billion to about $13 billion before being cut back to 2001 levels in 2006.
Non-defense R&D initially increased due to a 5 year initiative 1998-2003 (begun during the Clinton years) to double funding for the NIH from approx. $14 billion to $28 billion. After this point NIH funding (which accounts for half of non-defense R&D) stagnated. Non-defense non-NIH funding has remained essentially unchanged since 1992 (or for about 15 years).
While Bush has greatly increased the size of the federal budget, during his tenure funding for basic research which has been the foundation of our technological preeminence has languished or been cut. Democrats since taking control of the Congress have made some moves to increase funding in the 2008 budget.