I saw old thread discussions on this topic, and thought it would be fun to revive the topic.
Can severely damage if not one-shot the stronger ships in the game (strongest non-death star attack)
Can take a punch too (a little weaker than a destroyer)
The only defense that is protected from deathstar rapid fire
Expensive - You can build a lot fewer than gauss cannons (depending on how you value resources, 5 to 1), this means fewer plasmas will be defending than the potential number of gauss cannons
Hits a little harder than a battleship, so an excellent choice against mid-tier ships (can one-shot cruisers)
Can build in larger numbers (maybe 5:1 as described above)
Bombers do not have rapid fire against, so a good counter to bomber fleets
Not too tough - battleships can take more damage (although equal number of gauss still beat battleships due to higher firepower)
deathstars do have rapid fire against
One thing that I read is that if your defense has a vulnerability to a certain type of attack, you can expect to receive that type of attack. So I think the best approach is to build both. If you build a gauss cannon only attack, you can expect deathstar raids since you can't counter the rapid fire. However, if you build only plasma cannons, you can expect swarms of weaker ships to limit the damage done by the plasmas.
If you are looking for a small defense, I think plasmas are the better option. You know that there are fleets out there that can crack your defenses. You just want to get a few lucky hits to destroy some of their ships so that there is a cost to attacking you.
If you are looking for a strong defense, one that will fight to a draw even on the big guys, I think gauss cannons are more important (still need at least some plasmas for deathstars). There also seems to be a line. If you are facing battleships and lower, it seems like gauss cannons are the better choice. If you are facing battlecruiser or better, plasmas are the more economical choice. Gauss cannons are at their best when facing a large number of cruisers (which I have noticed is not uncommon at the higher levels). When fighting battlecruiser and above, the edge goes to plasma cannons.