I've heard that Virgin and the cheaper flights don't land at the main airport, but one like 70km out of town, you may want to take that into consideration.
Jetstar lands at both Avalon and Tullamarine. U can get cheaper flights if u land at Avalon, which is a fair drive outta the city (about an hr depending on traffic) or slightly more expensive if u wana land at Tullamarine which is about 15-20mins drive from the centre of melbourne.