Note that this thread is primarily concerned with shipbuilding aesthetics. I won't be covering anything on weapon modification or ship balance, as those fields would be better covered by others, and are more subjective. While arguably aesthetics are also subjective, there are certain things that either almost always look bad, or could be improved upon with a little effort. Let's get started, shall we?
First off, here's an example of a big don't. I don't care who you are, or what you're making, this never, ever looks good, and can always by improved upon:

This is one that I've been seeing a lot of lately, and it really isn't good. One section - particularly that section - tiled over and over again, in almost the completely same size, in the completely same pattern. Even if you somehow manage to make it look good, with a few changes, you can make it much better.
Let's try a few different things to see if we can get it looking better. First, perhaps we'll resize some of the sections, and maybe flip them around a little.

Damn. Just a few size changes and a bit of flipping and that already looks a lot better. But it's still sort of repetative. Let's try a bit of section rotation, next.

Hrm, it certainly removed a lot of the repetition, but with that same section tilted all over the place, it looks kind of messy. Let's go back to the second pic, and instead of just rotating sections, we'll try also removing some, and replacing tham with other sections, for added variation.

Complete transformation! The original ship has gone from being blocky and repetitive, to being a fairly unique looking ship, while still retaining most of the feel of the original. On larger ships, you can get away with more tiling, but I personally suggest only doing two or three rows at most, of tiling the same section, and then breaking it up with some other sections. Use of colours is also very helpful in make a ship look less repetitive.
Anyway, that's all for this post. I'll update with more sometime soon. Perhaps in a few hours, perhaps in a few days, depending on my mood, and how busy I am. If you have anything you'd like to add, or any useful criticism or commentary, feel free to throw it my way.