A few years of playing the The Sims series taught me one crucial thing: Never build rooms without a purpose. That is certainly so in Minecraft too. Note that this post gives tips on general layout, not necessarily pretty details. Still, after having built and used a fair number of frustratingly laid-out bases (Strongholds are the worst offenders of this, ever), I can definitely attest that layout is a very important factor in your base's likability.
Simply stacking boxy rooms next to/on top of each other does not make a pretty base. Before you start building, you should ask yourself a question or two. For instance, "What should the reactor/enchanting/cookie baking room look like?". Then, design the room with the purpose in mind. It's a lot better than building a base first, and then awkwardly trying to shoehorn in a setup in whatever idle room you find. Or worse, leaving the rooms empty because you can't find a purpose for them.
Try to begin with the end in mind. What kind of rooms do you need? What should they contain? Which rooms should lie next to each other for maximum convenience? For instance, you'd want your storage room to be close to your ore processing line, to avoid having to string pipes everywhere. Likewise, power generation should be close to the machine room. There should not be a maze of corridors between your bedroom and the room where you spend most of your time, if you go to sleep every night. Similarly, seldom-used rooms (for instance, housing Implosion Compressors, Enchantment Tables or BC laser setups) kan be kept away from the central part of the base. Having to run around the Assembly Table every time you walk between your machine room and your depot will get really annoying after a while. Speaking of really annoying, keep your cow farm far away from everything else. Your ears will thank you.
In the process, don't be afraid of ripping up your entire earlygame setup when upgrading your base. That wall of Iron Furnaces will serve no purpose once the Induction Furnace is running. Stacking more and more chests to store ores and ingots in your machine room works in early-mid-game, but eventually you're going to need a separate depot (or convert to AE). That library you've got can be rebuilt elsewhere if it stands in the way of your Molecular Assembly Chamber.
And with function, beauty usually follows suit. Integrate the purpose of the various rooms into your design, rather than designing separately from the purpose. If you know you're going to need a Nuclear Reactor, for instance, build a mini power plant around it. Shielding walls, a control room, perhaps even a particularly well-protected chest to store valuable stuff in when tinkering with the reactor. Your reactor might be totally safe, but that storage room provides an extra level of depth to your design. Same goes for your base entrance, why not put in a reception desk?
In short, lay down a basic map of your base in your mind before building it. It might also be a good idea to leave room for expansion, for instance having a pretty little garden outside your depot so you don't have to demolish anything other than a flower bed when you eventually run out of room in there. Less important rooms can also be stacked vertically, for instance in towers or dungeons. If you only use your Assembly Table to make a Gate every other week or so, the setup can be placed in some far-off corner of your base.
Last, throughout different stages of the game, your base will have different requirements. Your initial dirt-and-planks hovel won't need to house much more than a furnace, a crafting table and a few chests. You will have to build new rooms as the game progresses, and unless you're super-efficient at reuse, you will discard a few rooms on the way too. My tip then is to rebuild, not expand, once you feel that your requirements have changed sufficiently from the last phase. Trying to keep your hovel as the centre of your high-tech base is going to require a lot of skill to pull off properly. It's better then to abandon it or tear it down, and build something epic from the ground up.
