The use of Instruction Set Extension (ISE) in customising embedded processors for a specific application has been studied extensively in recent years. The addition of a set of complex arithmetic instructions to a baseline core has proven to be a cost-effective means of meeting design performance requirements. This thesis proposes and evaluates a reconfigurable ISE implementation called “Configurable Flow Accelerators” (CFAs), a number of refinements to an existing Automated ISE (AISE) algorithm called “ISEGEN”, and the effects of source form on AISE. The CFA is demonstrated repeatedly to be a cost-effective design for ISE implementation. A temporal partitioning algorithm called “staggering” is proposed and demonstrated on average to reduce the area of CFA implementation by 37% for only an 8% reduction in acceleration. This thesis then turns to concerns within the ISEGEN AISE algorithm. A methodology for finding a good static heuristic weighting vector for ISEGEN is proposed and demonstrated. Up to 100% of merit is shown to be lost or gained through the choice of vector. ISEGEN early-termination is introduced and shown to improve the runtime of the algorithm by up to 7.26x, and 5.82x on average. An extension to the ISEGEN heuristic to account for pipelining is proposed and evaluated, increasing acceleration by up to an additional 1.5x. An energyaware heuristic is added to ISEGEN, which reduces the energy used by a CFA implementation of a set of ISEs by an average of 1.6x, up to 3.6x. This result directly contradicts the frequently espoused notion that “bigger is better” in ISE. The last stretch of work in this thesis is concerned with source-level transformation: the effect of changing the representation of the application on the quality of the combined hardwaresoftware solution. A methodology for combined exploration of source transformation and ISE is presented, and demonstrated to improve the acceleration of the result by an average of 35% versus ISE alone. Floating point is demonstrated to perform worse than fixed point, for all design concerns and applications studied here, regardless of ISEs employed.