Base hub with all sub-Compact Machines, storage, machinery, etc. It was certainly a good idea to have as much as possible in the cubes as teleporting from cube to cube is almost instant since all cubes are in the same dimension. Also, I had zero lag in the cubes unlike outside in the deep dark.
Storage area of my Ender Quarry. The last Quarry I've built was 1000x1000 blocks with Speed III and Silk Touch Upgrade. SFM was fast enough to handle the massive amount of incoming ores and junk via Ender Chest.
AE2 Processors and Pure Crystals automation with SFM Block Gate and Rapid Item Valve.
My Big Reactor was 9x9x9 filled with Gelid Cryotheum. Reactor Control Rods set to 50% and producing 50k RF/t. It used a lot of fuel but there was no need building turbines anymore with the excessive amount of Yellorium from the Quarry.
Oak Wood tree farm with Farming Station, Flux-Infused Axe and Reinforced Watering Can produced massive amounts of Wood in no time.
Wool farm with Stone Animal Farmer and Shiny Shears. It wasn't very efficient for the 16k+ Wool needed for the quest but I got there eventually. On a side note: Shiny is one of the best materials for Tinkers' Tools and a stack of Shiny Ores is given from one of the first few quests. Shiny does the most Attack Damage has great durability and the same mining speed as Cobalt.
Food and tree farm automation with Bone Meal and Autonomous Activator (and Farming Station for trees). I've had a normal crop farm in a maximum size cube with 3 floors and Golems before but it was too slow.
Basic mob farm with Cursed Earth, Fans, Diamond Spikes, Vacuum Hopper and Bedrockium drum for the XP. On top I've planted Silver Wood Trees to get Pechs spawning. I've added a Witch (for Glowstone Dust) and Enderman Powered Spawner later once I had my Big Reactor going.
Basic AE2 auto-crafting. Very small but all I needed.
More AE2 auto-crafting, I didn't even need the Transvector Interfaces.
Thaumcraft automated infusion for the Lamps. Piped in the items from the bottom floor into the Arcane Pedestals and Autonomous Activator with a Tome of Knowledge Sharing and a wand next to the Runic Matrix to automatically activate it.
Alchemy automation with Golems for Alumentum mass-production.
It was worth finishing the "Supplying the Masses" quest line for Thaumcraft before going into KAMI to get the fully charged Ichorium Wand and Aura Nodes from the reward. One thing I didn't know before: Energized Aura Nodes with minimal aspects are still quite efficient for recharging wands. One node and only 2 aspects of each type will always give a value of 1 when energizing it producing still about 12 vis per minute for each type which isn't bad at all.
Final infusion for the "Ichorium Infused Hyperenergetic Singularity of Light" to craft the Deep Dark Portal.
Yes, I was not kidding about getting Bedrock for the Turret Configuration quest.
Some custom recipes I've used for Ender/Nether Shards and Amber which I could barely find if at all.