Difference between Altera Modelsim and Modelsim by Mentor?

the Quartus II Simulator is really an 'older' tool at this point meaning it does not support the newest device familes. it is largely graphical waveform based, as mentioned it cannot use HDL test benches. there is a tool to create HDL from your legacy vwf files.

there are actually 2 'Altera' versions of ModelSim. there is ModelSim-Altera Starter Edition (free) and ModelSim-Altera Edition (pay). the comparison between these two is as follows:

http://www.altera.com/products/software/quartus-ii/modelsim/qts-modelsim-index.html

some of the features of a ModelSim non-Altera have been highlighted here. another example is that ModelSim-Altera Edition does not support mixed language simulations.