Since almost everything except Thaumcraft required energy (MJ or EU) to power most of the machine, I would suggest to set up a forestry tree farm (go look at sengir forestry site, it contains allt the basic information you need especially the farm structure and shape). It is a bit ressource demanding to start up, but once establish, it will provide with a strong, renewable energy source, with low maintenance.
Also, it does not require too many different resources: copper, tin, iron, redstone a few diamonds and some gold.
Here is how it will work and what you will need:
- For the farm, start with a small size farm (3x3x4=36 farm blocks), which will allow you to have a 72 blocks crop. If you have more ressource, then consider the 3x5x4 farm (demanding 60 farms blocks for a 156 blocks crop).
- Each farm block is simple to make, but making 36 of them takes up ressources, as you will need 2 copper ingots, one tin electron tube, 2 wooden slab and 1 stone brick, or 1 bricks or smooth/chiseled sandstone (all 36 blocks needs to be of the same block)
- To make the tin electron tube, you will need to build a thermionic fabricator (a simple machine from forestry), which you will have to power will a little bit of energy, typically a stirling engine should be enough. You will need glass to run the thermionic fabricator and redstone and tin ingot to make the eletron tube (2 redstone and 5 tin ingot will give you 4 tubes).
-You will need to make a three specific farm block (farm valve, farm hatch and farm gearbox), but those are simple to make once you have the basic farm blocks
Once you have made all those blocks, set up your farm!
You will need a either 72 or 156 (depending on your farm size) case block where your crops will grow, those blocks can be of many variety, but are not basic blocks (like cobblestone or stone).
You will also need the same quantity of dirt to start of your farm (but you don't need to lay it done, the farm will convert them in humus and lay it for you).
You will also need to find some sand and apatite to make fertiliser, and obviously some sapplings - ideal are apple oak sapplings. Apatite is not so easy to find, but once you hit a veins you will have more than enough for a while.
We are almost done, you will need a pump to water you farm - if it is not a desert, you can try to water it initially manually with bucket of water until you can automate the water supply with a pump.
Then power the farm to start it - later the farm will supply its on energy, but initially, a combustion engine or a couple of stirling engine will be needed - maybe a clockwork engine can do the trick, I never tried since it is quite new.
Second step - the energy plant
Now that you tree farm is running, you will have abundant supply of woods and sappling. Both can be converted into energy.
Assuming that you have a apple oak tree farm (basic tree), you want a squeezer and a fermenter then at least one energy machine, a biogas engine (for MJ) to start with, then a bio generator (for EU) or more biogas engine.
You also want to automate a bit the flow of all those material, so you will need one diamond pipe, several wood pipe (basic, for liquid and for energy), cobblestone pipes, energy gold pipe and several redstone engine.
Connect a wood pipe to the farm hatch, then a diamond pipe to sort in three flows the output of the farm: wood toward a chest (for now), apple towards the squeezer, sappling towards the fermenter.
The squeezer will convert apple into juice with mulch as by-product. You need both. With the right pipe, feed the juice to your fermenter. Do the same with the mulch.
The fermenter will convert sappling into biomass. You need a liquid and mulch to do the conversion. As liquid, you can use water, but if you use juice, your yield increase by 50% and since you should have abundant apple, use it !
Finally, connect fermenter to the biogas engine. You will need a couple of lava bucket to start the biogass engine, but once it runs, it won't consume lave anymore.
The squeezer and the fermenter need MJ to run, so once the biogass is ready to run, connect it to both equipment and phase out the stirling or combustion engine you used to kickstart the line.
Congratulations, you are self sufficient with renewable energy!
Fine-tuning and improvement:
- adding a few intermediate tanks as buffer for the juice and biomass is recommended;
- balancing the flow of all output/input is a tricky exercise. With one squeezer, you will probably not be able to process all the apples, so a second one can be an option. You will definitely produce more mulch than you can handle, and frankly, I have not find a suitable use for it.
Where to go after ?
Well, you will quickly notice that one biogas engine does not absorb all the biomass than even a single fermenter can produce, so build more of them. The big advantage of a biogas engine is that it cannot explode! So go for it. You should be able to support at 7 biogass engines with the smallest farm, which will deliver about 35 MJ/t, enough to make quarry run at max speed and support a few other equipments.
Until the latest update of forestry, the largest farm tree (180 blocks crop) was supporting 28 biogas engines without problem, so quite enough to support many lasers for an assembly table.
You will notice also that you are producing large, very large amount of wood. You can convert all that into charcoal with a little bit of piping and automation with ovens. And all this charcoal can be used to power combustion engines to provide even more energy.
Once you have a large supply of energy, you can decide to do more or less what you want...