My kids absolutely love ACMI, whether there's a show on or not, there's always things to play with and fascinate the mind.
The Melbourne museum is always interesting and now free for kids and those with a concession card.
Science works is great and although e name eludes me (someone may blog in with the answer here) a venue similar to science works in bendigo.
We took a group of kids on camp to bendigo and their activities included: this venue, bendigo pottery (where they made things), bendigo roller skating, down central Deborah gold mine, on the talking tram car and the joss house just to name a few.
Back to Melbourne, how about fun fields, geelong water park, the Melbourne markets, I think they sometimes do a kids in the kitchen session.
In summer their night markets are fun.
Caribbean Market on Wednesday's and Sunday's, the wantirna markets on Sunday mornings.
My kids love walking through sassafras and visiting jepettos workshop to admire the toys.
A visit to polly woodside, sometimes there's a sound and light show at the casino.
A trip on the teams around Melbourne (free city circle tram)
The list goes on and on, hopefully that's added a few.