National Clean Energy Superhighways Act of 2009

National Clean Energy Superhighways Act of 2009 - Amends the Federal Power Act to: (1) authorize states of the Eastern interconnection and the Western Interconnection to establish interconnection-wide multistate transmission planning (MTA) authorities; (2) require the Federal Energy Regulatory Commission (FERC) to establish procedures governing MTA certification; (3) direct each MTA to exercise sustainable transmission grid (STG) transmission planning functions for its region and produce a biennial STG transmission plan that identifies needed STG projects and areas to be avoided in siting of STG projects; (4) require the Commission to develop an interconnection plan if no MTA for the Eastern or Western Interconnection is certified within a year; (5) direct MTAs to ensure that multiple certified plans are integrated with each other; (6) permit MTAs and states to recover costs for planning activities pursuant to a transmission surcharge that the Commission is required to establish under this Act; (7) authorize MTAs within an Interconnection, jointly, to submit an integrated Interconnection-wide cost allocation methodology; (8) give the Commission authority over regional planning entities to implement planning efforts, except the Electric Reliability Council of Texas and entities in Alaska and Hawaii; (9) require public utilities to apply to the Commission for a certificate of public convenience and necessity in order to construct or modify an STG project; (10) require STG construction certificates to incorporate a condition that prohibits the direct interconnection to the STG transmission line by any electricity generator that has a greenhouse gas emission rate greater than that of a singe-cycle natural gas-fired combustion turbine; (11) terminate such condition upon the implementation of a greenhouse gas regulatory program applicable to the electricity sector; (12) set forth provisions concerning exercising eminent domain to acquire the necessary right-of-way and property necessary to construct, operate, and maintain STG projects and long-term transmission rights; and (13) direct the Commission to encourage methods and structures for grid operations to better accommodate renewable energy resources.

Requires the Department of Energy (DOE) to analyze, recommend, and report to Congress on metrics for transmission grid performance covering transmission grid facilities.