I have been doing some research on which car ferries are still running as at June 25 2012.
It seems that Virtu now have a monopoly. Their service from/to Pozzallo is now the only way by car to/from Malta. Thre is no service by car to/from Catania, as the Catania connection is only by bus for foot passengers via Pozzallo.
Grimaldi Lines seem to have ceased their sub-contract with Translubeca (although we used this as recently as early May) when there was a weekly service from Catania to Malta. Shame, as it was a lovely trip.
GNV no longer operate to Malta (but oddly they have still kept their Tunis operation).
TTT Lines run from Naples to Catania nearly every day.
From further north, GNV still operate Genoa/Palermo, Livorno/Termine Imerese and Civitavecchia/Palermo.
If you have time on your hands, you can still drive through Corsica, Sardinia and Sicily. We did this last Autumn. There are frequent ferries from Toulon or Nice to Corsica, several short 50 minute crossings from Corsica to Sardinia every day, then an overnight from Sardinia to Sicily every Friday.
But with such reduced competition compared to 1-2 years ago, prices are high!