Here's my base in Magic Farm 2. I'm working my way through the new thaumcraft content at the moment. This is still very much a work in progress, but I feel it is coming along far enough to share with the rest of the world.
The outside of my tower. I still have to clean up a few items like the harvestcraft beehive floating in mid-air.
Here are my harvestcraft farms as well as my growthcraft grape farm. I have an upgraded flesh golem harvesting all the grapes (3 range upgrades). The grapes are used to power my base by feeding a culinary generator. I don't have much in power requirements at the moment, so I'm sure I will have to diversify, but this works for now. The growthcraft grapes grow so well, I haven't yet really made a point of harvesting my normal crops on a regular basis. Once I get some more TE and MFR set up, I will likely make use of the other food choices and make more specific farms for energy production. I'm using the food challenge configs, so my only energy choices are food and plant based.
Next up is my infusion room. This is where most of my effort has gone into creating. I still have a few hoppers to place, along with some candles, but for the most part, it is built out. I'm not really liking the torches everywhere, and dislike the dark ceiling, so I will likely place some gaseous glowstone in the room to brighten things up a bit. So far, the stabilising effects around the infusion alter have been enough. I haven't had any flux effects except for one moderate enchantment I have done.
I'm sure you noticed the lack of any essence jars in my infusion room. I setup the essence production and storage directly below my infusion altar. I do have to go below and verify that there is enough essence before I start an infusion crafting, but it's a small price to pay for not having a golem running around getting stuck on everything. I had thought I would have to use an essentia mirror, but apparently the range of the altar is enough to pull the essentia up from the room below. I placed a few inverted stairs to give a good place to place my mob heads. Every little bit of stability helps. I found out that a single alembic is all I need for the essentia distillation. The jars will be rearranged and labelled along with a void jar being placed on top for handling excess essentia.
Finally, I have my wand recharging station and soon to be osmotic enchanter. I need to collect a few more obsidian totems to build out the pillars as seen here. (I used a few of the tiles for the screenshot.) The block in the middle is where the enchanter will sit. I've only managed to jar 4 nodes at the moment. I have all the elements, just not as much of some of them as I would like. This will be taken care of at a later date, or when I finally make time to get it done. The floor being built above will contain something. Just not sure what quite yet.