This changes over time for the galaxies. If I'd say Magnetic Towers (blue) this is not helpful because you get one maybe on the second galaxy, more even later.

For the weapons over a whole playthrough, my style:

* Laser Cannon (red): First galaxy, half of second galaxy, then rarely again. 10-12 are typically enough.
* Missile Launcher (red): Always used up to endgame. Can be placed anywhere in any direction filling gaps.
* Twin Blaster (red): Yes please! First comes after half of first galaxy, you can obtain around 2-3 in the first galaxy, getting more in the second. I aim for around 5-6. Placing them in all six edges allows to concentrate firepower nicely since they can be switched for directions covering 3 of 6 angles. Becomes obsolete for me around half of third galaxy.
* Mine Launcher (red): Becomes available after 1/3 of second galaxy. Huge damage, tanks hits, nice overload ability. I use them up to half of third galaxy, 2-3 are enough.
* Laser Machine Gun (red): Available around last third of second galaxy, more in the third galaxy. I use them only rarely but they can be helpful in Bossfights for sniping with their ability. 2-3 are enough for me and they have a short window since I skip them after around half of third galaxy.
* Heavy Missile System (red): Comes around in third galaxy. 1-2 are enough for me. Nice damage, especially against large asteroids, wide arc but missiles need time to hit the target - I prefer Magnetic Towers instead which arrive around the same time (they hit instantly).

* Ion Cannon (blue): 4-5 can be used in the first galaxy for some encounters and there are some cargo routes in the second galaxy where they shine, but after that they are rarely used by myself.
* Magnetic Tower (blue): My favorite. Comes around third galaxy and its hard to get enough of them and a large enough ship to place them before fourth galaxy. But they can make most runs trivial later. I aim for around 6 in endgame.

* Plasma Cannon (green): I skip them.
* Plasma Missiles Battery (green): I use them sometimes to fill gaps, around 2-3 in the second galaxy. Their ability is nice against large bosses and many small asteroids, but same problem with rockets - they need time to hit.
* Void Cannon (green): I skip them.

I know others play differently, so the opinions can vary. ;-)

Early game just build towers, supporting them with upgraders where possible (e.g. three red lasers in front, a shared upgrader behind, followed by three missile launchers behind). Going to midgame, you want connectors in lines, so upgraders/shield effects are transported over a whole row of weapons instead of building upgraders/shields again and again everywhere.
Mid-/lategame your ships have connectors around your whole ship, single connection (mostly) covering any module. So the whole ship shares the same 2 green/red/blue upgraders, the same shield(s) etc. leading to massive firepower and defense - overloading an upgraded Protected Aegis gives your whole ship invulnerability that way for around 10 seconds restoring whole shield after effect ends... since most tough fights do not last that long, its basically easymode especially for bosses.

Originally posted by BinaryBrain:

This changes over time for the galaxies. If I'd say Magnetic Towers (blue) this is not helpful because you get one maybe on the second galaxy, more even later.

For the weapons over a whole playthrough, my style:

* Laser Cannon (red): First galaxy, half of second galaxy, then rarely again. 10-12 are typically enough.
* Missile Launcher (red): Always used up to endgame. Can be placed anywhere in any direction filling gaps.
* Twin Blaster (red): Yes please! First comes after half of first galaxy, you can obtain around 2-3 in the first galaxy, getting more in the second. I aim for around 5-6. Placing them in all six edges allows to concentrate firepower nicely since they can be switched for directions covering 3 of 6 angles. Becomes obsolete for me around half of third galaxy.
* Mine Launcher (red): Becomes available after 1/3 of second galaxy. Huge damage, tanks hits, nice overload ability. I use them up to half of third galaxy, 2-3 are enough.
* Laser Machine Gun (red): Available around last third of second galaxy, more in the third galaxy. I use them only rarely but they can be helpful in Bossfights for sniping with their ability. 2-3 are enough for me and they have a short window since I skip them after around half of third galaxy.
* Heavy Missile System (red): Comes around in third galaxy. 1-2 are enough for me. Nice damage, especially against large asteroids, wide arc but missiles need time to hit the target - I prefer Magnetic Towers instead which arrive around the same time (they hit instantly).

* Ion Cannon (blue): 4-5 can be used in the first galaxy for some encounters and there are some cargo routes in the second galaxy where they shine, but after that they are rarely used by myself.
* Magnetic Tower (blue): My favorite. Comes around third galaxy and its hard to get enough of them and a large enough ship to place them before fourth galaxy. But they can make most runs trivial later. I aim for around 6 in endgame.

* Plasma Cannon (green): I skip them.
* Plasma Missiles Battery (green): I use them sometimes to fill gaps, around 2-3 in the second galaxy. Their ability is nice against large bosses and many small asteroids, but same problem with rockets - they need time to hit.
* Void Cannon (green): I skip them.

I know others play differently, so the opinions can vary. ;-)

Early game just build towers, supporting them with upgraders where possible (e.g. three red lasers in front, a shared upgrader behind, followed by three missile launchers behind). Going to midgame, you want connectors in lines, so upgraders/shield effects are transported over a whole row of weapons instead of building upgraders/shields again and again everywhere.
Mid-/lategame your ships have connectors around your whole ship, single connection (mostly) covering any module. So the whole ship shares the same 2 green/red/blue upgraders, the same shield(s) etc. leading to massive firepower and defense - overloading an upgraded Protected Aegis gives your whole ship invulnerability that way for around 10 seconds restoring whole shield after effect ends... since most tough fights do not last that long, its basically easymode especially for bosses.

Thank you so much for the detailed information.

Any tips on what ship is the best? I mostly enjoy lots of space for cargo to save me going back and forth.

For the ship, my rule of thumb is: More BASE cells is better. Extra cells are nice but you will often not fill all of them (they can be expensive to craft and the crafting becomes quickly bottlenecked by level of the crafters). A high max cell number of the ship is also nice.

For me, in early game the epic ship "Free Bird" is a noob trap for example - it has a huge amount of extra cells (67) but only a few base cells (10). Lets assume that you bought 20 extra cells at the crafter, this leads to a ship with 10+20=30 cells.
Compared to e.g. the epic ship "Ghost" (costs same, can be bought at same trader) with only 30 extra cells and 25 base cells, you get a ship with 25+20=45 cells.

I'd say that layouts of ships rarely beat more cell ships for the first 80% of the game (in endgame with close to maxed crafts you can design weird ships hyperfocused for certain strategies of course).
More cells = more cargo or modules built = easier and more efficient runs.

For ship class I I would go for the Ranger (2500 credits) or the rare Wanderer (5000c). The epic T-Hunter is nice but expensive (20.000c) and can be replaced soon, so I would skip it. For ship class II I would aim for the mentioned epic Ghost (40.000c) along with as many extra cells as possible, it can carry you up to the first few runs in the second galaxy. With its centered gap you can place thrusters on the inside of the ship, leaving more space for laser weapons on the outer side.
Sometimes (rarely) you get ships from a successful run, also some that are not available from traders, but I would not count on getting them.