Benjamin H. Friedman makes a strong case for funding wars within the defense budget:

[P]utting war funding in the Pentagon budget means that other defense programs get cut to make way, heightening tradeoffs among military objectives. That requires strategy. Robert Gates brags about forcing the Pentagon to sacrifice long-term priorities to fund today’s wars. But what’s extraordinary is the limited nature of his efforts and the Pentagon’s ability to avoid changing its priorities amidst two wars.