Primer3 is a widely used program for designing PCR primers. Primer3 
can also design hybridization probes and sequencing primers. PCR is 
used for many different goals. Consequently, primer3 has many 
different input parameters that you control and that tell primer3 
exactly what characteristics make good primers for your goals.

For details and citation:
Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for 
general users and for biologist programmers. In: Krawetz S, Misener S 
(eds) Bioinformatics Methods and Protocols: Methods in Molecular 
Biology. Humana Press, Totowa, NJ, pp 365-386