Since I don't know where such guides might be, I'll give a few pointers drawn from my own experience (keep in mind that these are coloured by opinion/subjectivity.) Also, in case you're unaware, there is an in-game encyclopaedia that you can refer to, though while it gives specific numbers, it doesn't advise on usage scenarios.
Weapons: This is perhaps the most subject to personal preference - it's really about how you prefer to fight. As I prefer to command ships to fight on my behalf rather than to dogfight myself, my views here are pretty restricted. I favour high rate-of-fire weapons against small targets (the Particle Repeater Mk.3 is my default weapon), but the Inertial Hammer can be very effective. Plasma weapons are alright for taking out surface elements on capital ships (as it the aforementioned Inertial Hammer, with the added bonus that its damage continues onto the shields/hull), as well as for just wearing away a capital ship's shields or hull. If you prefer a sniper style, then the Railgun is for you (assuming you're playing with the Home of Light expansion.)
Missiles: These have been balanced in a perhaps somewhat odd manner - you'll find few situations where a missile that does enough damage to "one-shot" an enemy (fighter) is also fast and nimble enough to chase it down, with the exception of Starflashes vs Interceptor Drones. Against fighters, I typically use Sunstalkers and Astrobees, while Hellbusters and Tristars are excellent for taking out surface elements on capital ships (the latter wipe out entire clusters, if you fire them at the centre-most element.) I don't use Novadrones myself (but my Balors certainly do!
), but if I were to, they would be mainly for taking out surface elements on weapons platforms.
Drones: Sadly, drones' usefulness is very limited. Drones carried on my Albino Skank are generally a hacking drone (Trojan) and a scanning drone (Beholder), 4 shield support drones, and perhaps a couple of Intrepids or Interceptor IIs (the latter are really the only ones that can keep up with me, as I favour supercharged engines - but I VERY seldom use the combat drones. Some players use Traitor Drones to attach demolition charges to unsuspecting targets, but I have no experience with these, so I can't comment.
As far as drones operated by capital ships, unfortunately there are a couple of factors that make them less than amazing: firstly, the player has little to no control over their deployment and targeting; secondly, although ships can carry them in large numbers, they only launch a few at a time, which means you can't really overpower your enemies with a sizable swarm of drones, instead wearing away, but taking heavy attrition to your drones at the same time; lastly, drone casualties (largely due to the first two points) tend to be unacceptable, which combined with the ball-aches involved in replacing them makes them somewhat impractical - but... Drones used on your capital ships when you're not around work considerably better, as they add strength to your ship in an abstract manner, and are then not subject to attrition due to individual stupidity and what-not. So it's still a good idea to fit them when you can comfortably afford to do so
. For purely role-playing and aesthetic reasons, I tend to fit a mix of Interceptors, Intrepids, and Overruns, so that at least notionally my ships are equipped to deal with all enemy types. NOTE: Assault Drones (I think that's what they're called) don't work as described - in fact, as near as I can tell, they don't work at all.
Firstly, "how to best set them up with equipment" - well, unfortunately there's nothing to say here because ships only have one possible load-out each: you don't get "either-or" choices to make, other than whether to fit a shield or weapon, or not - the correct answer is almost always "yes, fit i" (exceptions would be very specific, rare, and specialised.) Ditto personnel: you NEED your ships to have captains, and you very much want them to have engineers; some players don't hire a defense officer on some ships to "prevent them from getting into trouble", but I find it's better to install a defense officer and simply make sure he/she is carrying out the appropriate stance order.
Firstly, it's quite easy to underestimate the value of M-sized (sub-capital) freighters - don't. Certainly for servicing your stations, these are superior in a number of ways (many of them subtle.) They are cheap, require only one crew (pilot) and a cheap one at that, and they dock/undock and load/unload far faster than capital traders. Also, and especially for stations that use/produce numerous wares, it's better to have, say, 3 M-sized containerships than one capital-sized one: the small ones can split up and each be buying or selling a different ware at the same time, instead of the large one having to deal with them one at a time, and often getting hung up on one "important" ware and neglecting the others (not to mention travelling around with only a fraction of its hold filled - what a waste!)
However, you WILL want capital-sized freighters at some point, and for certain tasks. For instance, when carrying large cargoes, especially over long distances (inter-sector, or inter-system), you'll want the benefits of a large hold, thick shields, defensive weapons, and the jumpdrive. And even stations can benefit from having some capital-sized freighters in addition to their smaller brethren. The smaller freighters, if crewed by skilled pilots, have surprising self-preservation, but capital freighters tend to be better, because they can boost away from trouble for longer distances, or jump away altogether, while their thick shields buy them the time to do so.
Here we're back to highly
subjective territory. Some players like smaller and faster ships in numbers, some players like heavily armed behemoths, yet others (me included) like to mix it up heavily. A ship I'm (perhaps inordinately) fond of is the Stromvok, at least in the early to mid game (later on, I still use them - affording them becomes trivial, in any case), and I'm a fan of the Taranis. Personally, I don't generally go heavier than Olmekrons for bringing heavy firepower, as I simply don't have the patience to wait for something like an Arawn or a Fulmekron to lumber its way to the destination, not to mention the havoc it can cause to ships trying to escort it, getting in their way constantly - but that's just me. I like ships that use Plasma Jet weapons, hence my fondness of Taranis and Ollie, and ships that are quick, hence I also favour Stromvoks, Light Suls, and Balors (this last is also an excellent choice for personal runabout ship, as it's quick and nimble, for players like me who prefer to get chauffeured around instead of personally flying to every destination.)
If you get more respondents, it's likely (nay, certain!) that you'll get differing and even conflicting advice - so much in the game is subjective rather than objective (which is good - if there were too many clear "best options", what would be the point, right?)
PS: There's MUCH I haven't covered - more than I have, in fact. Just so you know...