Getting stuff to where it needs to be is often a problem in Minecraft. EnderIO solves that problem impressively elegantly, by adding compact conduits that carry fluid, items, power and redstone signals. It also has a few machines that enhance your ore processing capabilities, too. When your base starts getting complicated, EnderIO is one of the best ways to sort it out. Grab it here.
Applied Energistics 2
Storage can also become an issue when you start automating more and more aspects of Minecraft. Applied Energistics solves the problem by turning the matter in your chests into energy, which is then stored on disk drives, accessible wirelessly from anywhere in your base. You can even use it to autocraft anything you need by interfacing directly with your machines. If that sounds a bit magical, you wouldn't be wrong. It uses vast amounts of power, of course, but once properly configured you'll come to see wooden chests as hopelessly primitive relics of the past. Grab it here.
JABBA and Iron Chests 2
More storage mods, but this time focused on the early-game. JABBA adds easy-to-craft, upgradable barrels that can hold hundreds of stacks of a single item, while Iron Chests lets you upgrade wooden chests to hold more stuff. In the long run, you'll probably still want an Applied Energistics system, but these mods make the early part of the game so much more pleasant. Get hold of them here and here.
Extra Utilities & OpenBlocks
This pair of mods are a grab bag of immensely useful utilities with no real theme running through them. Extra Utilities adds a golden lasso for transporting friendly mobs, blackout curtains for keeping places dark, conveyor belts to move mobs around, and sound mufflers to quieten down your stables. OpenBlocks, on the other hand, adds sleeping bags, hang gliders, elevators, gravestones, rope ladders and building guides. Both are essential. Grab them here and here, respectively.
It's always refreshing seeing mods that try something a bit different. PneumatiCraft is a tech mod, but instead of power it uses air pressure. You'll need to build compression chambers, pipes and valves to make sure you balance the flow of air, and if you get things wrong an explosion is inevitable. If you get it right, though, the nifty gadgets that PneumatiCraft brings to the table, like air cannons and configurable helmets, are well worth the time investment. Grab it here.