I've only completed episode 1 so far so I can't say for certain what I like best yet. I played the shareware version of this game a lot back in the day and I loved the laser weapon that was only available in arcade mode there. I'm assuming it'll be available to buy at some point in the full version of the game.

My current weapon setup is Pulse Cannon for my front gun (I didn't find anything I thought was particularly better) and sonic wave for my rear gun. I also have Vulcan Shot Options for both my left and right sidekicks, though it's hard to tell if they do enough damage to justify the price.

What setup have you found works for you and why do you like it?

Laser
Sonic Wave
double Plasma Storm

+1 here

Flamethrowers, obviously.

Hyper Pulse Laser
Retroball (though any other decent weapon will do)
Plasma storm OR a-bomb

At the moment I'm fielding the below on playthrough1, which works fine with the generator (15000) I have:
Zica Laser
Wild Balls
Zica Flamethrower

I recall flying around with a carrotship shooting bananas back in the days, that was pretty powerfull.

Zica Laser
Micromines
Zica Superchargers

Though I also like:
Laser
Sonic Wave
Plasma Storm

Bananas. Lots and lots of bananas.

Zica all the way, this is one of my favourite setups too. Partial to the flamethrowers, though.

Zica Laser
Sonic Wave
No real preference for sidekicks

Ship Type: The Stalker 21.126
Front Gun: Zica Laser
Rear Gun: Rear Heavy Missile Launcher
Shield: MicroCorp HXS Class C
Generator: Gravitron Pulse-Wave
Left Sidekick: Zica SuperCharger
Right Sidekick: Zica SuperCharger

Best setup available in the game and overkill on bosses but also note this is on Hard difficulty, 1 Player Full Game.

Do you know: if you win Zinglon's Revenge you will be stuck in Arcade mode.

My final ship before the end of the game:

Ship Type: The Stalker 21.126
Front Gun: Hyper Pulse
Rear Gun: Sonic Wave
Shield: MicroCorp HXS Class C
Generator: Gravitron Pulse-Wave
Left Sidekick: Zica Flamethrower
Right Sidekick: Protron Cannon Tangerine


But anyway, try to get flamethrowers early on and when you get sonic wave, upgrade it faster than the front gun.

Here's the layout that my family and I agree is the best:
For the ship, I just go with whichever one available has the highest armour;
For sidekicks, I go for the Dual Shot Option;
For main weapons, I aim for the Laser;
And for the side weapons, I go for the Sonic Wave.
Oh, and for the super-special bonus powerup thing, I aim for the Soul of Zinglon(Although, situationally, the Flare can be a lot better, and if you're playing on higher difficulties, I hear that the Repulsor(?) and the Attractor(?) work the best, since, apparently, the other bonus ones tend to become pretty useless on higher difficulties).

My setup goes a bit like this:

Ship:Stalker Prototype C
Front Gun:Hyper Pulse
Rear Gun:Sonic Wave
Sidekicks:Zica Supercharger
Generator:Graviton Pulse Wave
Shield:Microsol HXS Class A
Special:Repulsor

That seems to be my winning setup