One of the new application guides with the V4.0 release is aimed at using EnergyPlus for compliance. It's very new, so the information is not complete but you might take a look at it. (it's available for separate download from the EnergyPlus web site - www.energyplus.gov if you don't want to download and install the whole system.
As to comparison of products (though not interfaces such as Visual DOE or DesignBuilder), you can look at a paper comparing and contrasting Energy Simulation Programs can be found here:
http://www.eere.energy.gov/buildings/tools_directory/pdfs/contrasting_the_capabilities_of_building_energy_performance_simulation_programs_v1.0.pdf
As this paper was published in 2005, it is out of date (at least with current EnergyPlus capabilities).
The feature highlights from EnergyPlus releases can be seen here:
http://apps1.eere.energy.gov/buildings/energyplus/pdfs/featurehighlights.pdf
You could also look at producing files from the Example File Generator (under interfaces on the website) though they target more looking at 90.1 compliance than LEED.