Interstellaria/Crew management

Weapons
Crew can deal damage without having a weapon, but they do more damage with one. Weapons reload when you board your ship or touch an ammunition clip. Since you can give a crewman a weapon even if he is away, you can have one crewman reloading weapons while the others fight. The cooldown unit used by crew weapons is about 1/10 of a second. There are a few unique weapons listed under Secrets rather than here.

Melee
The Knife is slightly better than the Needle Pistol in tight spaces. You can but it at Trade Co, Oloke, Paren, Delna, and/or New Terra for 350. The Hunting Spear probably does more damage in the long run. It drops on Oloke.

Pistols
The Needle Pistol is your first weapon, and its only advantage is its high ammunition. The Bow offers slightly more damage, but it has kickback and low ammunition. You probably will not find it before it becomes obsolete. The Standard Pistol has accuracy, but does not provide the expected advantage from its price tag. The Needle Rifle has increased range, but its low accuracy prevents it from always reaching it. The Old Empire Laser offers 2.5 times as much damage per second as the Needle Rifle, but less range and ammunition. This is probably the best pistol in the game. The Kaidun Explosives have a 50% damage bonus over the Old Empire Laser, but have very low ammunition. They are useful when you need damage quickly rather than when you need to maintain the damage.
 * Indicates a loot drop.

Spray weapons
The Shotgun does as much damage as the Old Empire Laser if all the projectiles hit, but it has lower range, accuracy, and ammunition. It also has kickback. Its best use is places where accuracy backfires, like ledges. The Shrap Gun reports much better stats, but it suffers from the same accuracy issue as the Shotgun, and its guard range is actually much less than it claims.

Rifles
The Anoa Long Gun does only as much damage as the Needle Pistol, but it offers the best range found in the early game. It works well on bosses when you have plenty of room and a Goo Gun. The Flash Gun and Old Empire Laser Rifle have similar stats other than damage. They do less damage per second than the Old Empire Laser, but they start dealing damage sooner. If you get tired of farming for Old Empire Laser Rifles, Flash Guns provide a decent substitute. The Lever Action Rifle has very low ammunition, but it recharges. It offers the same expected damage as the Old Empire Laser, but it can vary. The Assault Rifle usually does more damage, but it is hard to get more than one, since completing Station Horizon prevents extras from dropping. The Rocket Launcher and Sniper Rifle both do the same amount of damage and have kickback, but the Sniper Rifle offers increased range and ammunition. The Rocket Launcher can also deal knock-back.

Auxiliary weapons
The Riot Shield blocks damage for ~2.5 seconds before running out of ammunition, but slowly increases ammunition when not in use. It's nice when you don't have extra weapons, but you don't need to hang on to it. The Goo Gun prevents enemies from moving or attacking for a short time after each shot. It makes bosses much easier, especially if you can get two Goo Guns to alternate shots. The Kursha Electric Prod prevents enemies from attacking for a short amount of time. It offers no real advantage over the Goo Gun, since it runs out of ammunition quickly. The Seedling Darts deals poison just like Scorpions and Mantas. It can be used to penetrate armor. The Confetti Gun is rather useless. It only fires when an enemy is in range, but has no noticeable effect on it. The Flame Thrower burns enemies, dealing damage over time.