+1 on Holgate. And grab yourself some of 'The Temptress' choc porter while you're there. Yum.
Info on regional breweries:
Tourism Victoria Regional Breweries
Info on Melbourne breweries:
Tourism Victoria Melbourne Breweries
Sadly not a lot of breweries around Ballarat I believe. The concerntration of them is around Victoria's Alpine country (ie. Bright Brewery, Jamieson's, Mt Buffalo) and also our wine country in the Yarra Valley (White Rabbit, Coldstream and Buckleys). Some locals may be able to point you in the right direction and Ballarat being a big old goldrush town is sure to have an awesome historic pub or several.
In Melbourne most locals would say for Breweries Mountain Goat is the place - In Richmond so just out of Melbourne's CBD. Great beers, you can see the brewery while you drink (and tours available on occasion) wood fired pizza, bohemian uni type crowd and there's an awesome pub down river st around the corner with great craft beer and food if you get bored of that called the Royston.
Links to Mountain goat brewery:
Goat Beer
Link to the Royston Pub:
Royston
For views of the water and a beer James Squire Tavern at Docklands is also supposed to be a goer:
All I could find was this old review:
James Squire Docklands Review 2007
Mrs Parmas also has a fantastic reputation and stocks a load of craft beer:
http://www.mrsparmas.com.au/
You also have Portland Hotel (which brews beer for James Squire on site) in the CBD which has a bistro, and some good beers on tap at the moment.
Hopper.