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Software the best of free to download technical software to assist in transformer, inductor & choke design. Please go to the homepage link and search for the latest download link. 
Epcos Ferrite Design Program An extremely useful tool from Epcos which allows accurate air-gap calculations on E cores, THD distortion, core Power Loss, high frequency AC winding loss and inductance vs bias among many other. Also contains complete catalogue data on entire Epcos ferrite range. www.epcos.com
LTSpice Excellent Spice version from Linear Technology designed specifically for SMPS circuits. Includes non-linear magnetics models. Has a very active users forum. www.linear.com
Femm Powerful 2D Finite Element Analysis from David Meeker. Not the easiest to use but can provide very accurate results. Website contains a number of tutorials to get you started and there is a users forum. Well worth the learning curve. www.femm.info
Magnetics Inc Suite of designs programs from a leading core manufacturer. The Current Transformer and Common Mode Choke programs are very limited but the Inductor Design program is a very useful tool which allows comparison between MPP, Sendust and High Flux cores www.mag-inc.com
Micrometals Iron Powder choke design program. Has a great Analysis mode which allows 'what if' scenarios by changing core size, turns etc.    www.micrometals.com
Metglas Package of programs specifically for amorphous and nanocrystalline cores. www.metglas.com
PI Expert Power Integrations program calculates transformer designs to work with their range of switching ICs. Gives very detailed build data. www.powerint.com
SIMetrix Free version of Advanced Power System Simulation Software. Very powerful yet easy to use SPICE-based simulator. www.simetrix.com