I normally start with an end goal. The most recent one was a GT grinder, but I wanted to go and use a different route than I normally do for building. I wanted to power my base differently, and get more into bees than before. I got melons early on with a villager trade. From there, I made a squeezer to make seed oil to make apiaries and also run a biogas engine. This engine powered my TE ore processing systems. To be more effective with farming melons, I used golems. To get golems, I had to research in thaumcraft. while building my upgraded melon farm, I used the dead space in between the melon rows for sugar cane, carrots, potatoes and flax. The sugar cane went into plant balls and eventually into IC2 biofuel cells in a diesel generator into an MFE to power my grinder. While I was doing all this, I was constantly short of wood, so when I got 5 diamonds, I made a SC wood cart farm. I used the extra saplings and turned them into plant balls as well for additional IC2 power.
So, just pick an end goal, and slowly work towards it. I had lots of fun building and automating the different pieces along the way.
This next time around, I think I am going to make a 36 block HP boiler powered by bituminous peat. But since I don't like systems that aren't fully automatic and renewable, I will use a large RP peat farm to make it instead of the new forestry farms. I also saw the new applied energistics mod spotlight, and want to give that a go, so that is going to end up in my base as well. The smallest automatic crafting engine in applied energistics takes 80 gold to make, so this is definitely going to be a mid-late game setup, but I am going to work towards that.