Train-and-bike options from Melbourne:

1. Train to Kyneton. Cycle Kyneton - Trentham - Daylesford (1 day; hilly.). Check out the wood-fired oven bakery at Trentham. Daylesford has lots of little cafes and shops, and the Chocolate Mill is a chocolate shop in a strawbale building maybe 20km to the north of Daylesford.
Daylesford - Creswick - Wattle Flat - Ballarat or Ballan (1 day) then train back.

2. Train to Wangaratta. Cycle to Beechworth. Stay there or cycle on to Yackandandah. From Beechworth / Yack you can either head North to Wodonga (either direct or via Talangata) then to Rutherglen and back to Wangaratta (total 3-4 days). Beechworth is a pretty town and Rutherglen has wineries.
Or, you could get to Mount Beauty, cross Tawonga Gap (climbing), then to Bright, then Myrtleford. From there, either back to Wangaratta via Milawa (wine, cheese, mustard), or down the King Valley to Whitfield, then Mansfield (crossing the range again) +/- Eildon, then cycle back to Melbourne via Healesville.