A true-and-blue strategy for designing ships isn't my particular forte, but there are a few rules of thumb that I try to live up to. It depends on what's available to me, which in turn depends on what I felt like researching at that time.
I'm a fervent user of smaller hulls: tiny, small, medium. Large and huge are the true behemoths compared to the rest of my fleet. Tinies make up the largest part of my fleet, usually followed by mediums as anvils. Smalls don't really see that much use.
As for loadout, that depends on my alignment and the phase of the game. As a good guy, and pretty early in the game, I try to deck out each ship with at least one unique defense. With the tinies, this isn't always a terribly bright idea (as it usually allows for only one decent weapon to fit next to it), so they are the first to make the shift to faster + nastier.
As a neutral or evil, tinies are more like gunships. Defenses are too large to be efficient on tinies, so I fit on two or maybe three decent guns, some engines and let them rip. Their visual design is usually pretty simple and practical to show mass production.
Medium vessels are a different story. They are the capital ships of my fleet. They also define the speed, so I usually slap on one good or two lesser engines. When it comes to loadout, I check where it will serve its frontline duties. Mediums are big enough to carry more than one type of defense, especially if you're good-aligned, so I try to put on two different types that look useful.
Weaponry? As much as I can fit into the nut. If I find myself thinking “this is overkill”, I trade a few weapons for a different kind. Mostly, I'm heavy on beams (because they don't slither over the field like a green blob), but I can squeeze in a few mass drivers, just for a laugh. It's a pretty rude surprise, and most races consider it at least marginally unpleasant.
As for looks, I try to match the ship with the defenses. If it has shields but no armour, I make it look very fragile; if there is armour, I slap on a few extra layers of tough-looking stuff, and some “headgear” for the cockpit; point defense is more difficult, since I have to make it look agile (usually by rounding the design more, with respect to angular velocity).
Oh, and I usually add a ghetto-blaster system (cleverly disguised as a missile launcher so no-one takes offense) to laugh enemy escorts into oblivion. It's a style thing.
Hope it's a bit clear,
Tarbo