Jeez, where do you start?
One route you could make part of a multi-day trip is from, say, Healesville to Traralgon via Yarra Junction, Noojie, Fumina and so on. Lots of pretty trees, and the extra bonus of doing Vesper's Hill (the warm-up hill in the Mount Baw Baw Classic) amongst a number of other smaller climbs.
In the northeast, you've got the Great Alpine Road, and now the option of Falls Creek to Omeo via the Bogong High Plains Road. As a one-day ride, the Alpine Classic Extreme route (look it up on Cycling Profiles) is going to be brutal, but it'd be a great, strenous but not outrageous two-day ride.
Another beautiful road is from Mansfield to Whitfield - a decent cilmb, some great views, and not much traffic.
If you're looking for something slightly less hilly, there are some interesting routes around Lake Hume via Tallangatta, Granya, and Bellbridge. Also in that area is the northern stretch of the Omeo Highway from Mitta to Tallangatta, and some side roadsand icluding Yabba Road an(though that's got quite a lot of rollers on it) d the Dartmouth Dam road.
Theroutof the Stratford to Dargo Classic is also very pretty, and the last hill is a *real* challenge. The only problem is that it's pretty much the only road in and out. It'd probably be worth doing twice, though - ride to Dargo from Stratford or Bairnsdale, stay the night, do the hill in the morning then ride home.
There's also a lot of interesting routes to Melbourne's immediate northwest, around Daylesford.
Further afield, if you can bear the thought of going to NSW, one very challenging ride I've considered would be the Alpine Way, including Dead Horse Gap...