Gauss is amazing for PD and against lightly armored ships, but becomes a bit less useful against heavily armored ships.
I prefer mesons for my beam fighters. They don't have the damage potential of gauss, but they pass right through shields and armor. Fighting in a Nebula, where both sides are likely to have heavy armor, being able to bypass armor is pretty handy.
The only downside is they don't pair up with missiles or other beam weapons very well, since they have to punch through the armor and shields first. If you've already weakened a target with missiles (as in, penetrated most of the armor and dropped shields) you're better off with other types of beam weaponry that does more damage like Gauss or lasers. In a Nebula you can't use missiles anyway, so focusing on mesons works great there.
Microwave weapons are also handy when fighting an opponent with no or minimal shields - which is always the case in a nebula. If going up against large powerful ships, being able to instantly disable their fire control systems and sensors (effectively neutralizing them unless they manage to make repairs) can save a lot of your ships. Mesons will sometimes take out fire control systems too, but the damage isn't focused (they bypass shields though, so they can occasionally disable even heavily shielded ships).
For a nebula defense station I'd have mostly mesons with one fire control dedicated to microwave weapons. That fire control could sweep the enemy fleet, blinding all of them, while the mesons tear them apart. By the time their sensors adjust after the jump you could blind their entire fleet, then slowly pick them apart with mesons.
You could also keep assault shuttles at a jump and board ships in a dense nebula, since most ships would be moving slow in one.
I sometimes wish the game had some form of weapon for targeting enemy engines, so you could focus on it for a boarding specialized race. Right now slowing down big ships enough to safely board without destroying them is a matter of luck - if you happen to kill engines first you can disable them, otherwise you might blow the whole thing up. That way you could use a combination of microwave and engine disabling weapons to blind and stun an enemy ship, board them, make repairs, and use the ship yourself.