Macbook retina 15 3 external screens

You've pretty much got two options for two external monitors on a MacBook Pro:

A) Two Apple Thunderbolt Displays

This is the least flexible, but highest performing solution. Obvious drawbacks are the cost, and not being able to use your existing displays. This only works on Thunderbolt equipped Macs with a discrete graphics card (i.e. not the 13" MacBook Pro or any MacBook Air, nor the base Mini).

B) DisplayLink adapter

You can use one display directly connected to the Thunderbolt/Mini Displayport with an mDP-HDMI adapter, and run the second one with a DisplayLink adapter. DisplayLink is essentially basic graphics card connected to your computer via USB. Because of the limitations of USB, it's not a high performance solution - don't expect to do any gaming on it. This does allow you to use your existing monitors, and at relatively modest expense. You may also want to check the current status of Lion support, as I remember seeing some posts about bugs relating to DisplayLink adapters - they may have been fixed by now however.

You can indeed use both the HDMI and Thunderbolt ports to drive two separate monitors with a Mac Mini.

Any Mac with a Thunderbolt port can use any mini Displayport display, cable or adapter, so you're correct that the mDP to DVI adapter is what you need¹. If you have a display that requires dual-link DVI (typically only monitors with resolutions higher than 1920x1200), you'll need an active mDP to dual-link DVI adapter.

For the HDMI port, HDMI to DVI adapters are readily available (HDMI is essentially a superset of DVI with a different connector). Note that the HDMI port is limited to monitors with 1920x1200 or lower resolution.

_{¹ Note that the reverse is not true - Thunderbolt monitors can't be used with mDP equipped Macs.}