Note: This account that I am currently using does NOT belong to me, it is actually one of my friend's accounts that he let me use (as my computer is broken), so if you see me in proto equipment in the game, just remember that it isn't me. Anyways, I have been playing Spiral Knights for around a year now, and I consider myself an experienced player. Please comment below if you think there should be changes made to the guide.
Everybody, whether you're a swordmaster, gunslinger or bomber, should know the type of damage and weaknesses that every single monster family has. If you don't, then here it is:
Slime Family
Damage Type: Piercing
Weakness: Shadow
Beast Family
Damage Type: Piercing
Weakness: Piercing
Gremlin Family
Damage Type: Elemental
Weakness: Shadow
Construct Family
Damage Type: Elemental
Weakness: Elemental
Fiend Family
Damage Type: Shadow
Weakness: Piercing
Undead Family
Damage Type: Shadow
Weakness: Elemental
As you can see, it is better to prepare for all of these monster types, rather than just one or two. So it is best to have three swords of every damage type (piercing, elemental and shadow), and three sets of armor, helmet and shield protecting you against every damage type. (Note: As none of the monster families are weak to normal damage, I strongly suggest avoiding swords that deal normal damage, e.g Calibur. On the other hand, if you want a gun/bomb as a sidearm, I'd suggest getting ones that do deal normal damage, since they can be used in almost every situation - which is something you want if they are not your primary weapon.)
Weapons
Swords
For a sword that deals shadow damage (good against the slime and gremlin family) the best choice would either be the Gran Faust (if you like heavy, two-hit swords) or the Acheron (if you like 3-hit swords). Here are their alchemy paths:
Sealed Sword - Faust - Gran Faust
Brandish - Nightblade - Silent Nightblade - Acheron
For a sword that deals piercing damage ( good against the beast and fiend family) the best choice would either be the Final Flourish or the Barbarous Thorn Blade. At the start of their alchemy paths, which is the Flourish and the Snarble Barb, I believe the Flourish is cheaper and easier to get. But if you like the look/power of the Barbarous Thorn Blade more, then go for it! Alchemy paths:
Flourish - Swift Flourish - Grand Flourish - Final Flourish
Snarble Barb - Twisted Snarble Barb - Dark Thorn Blade - Barbarous Thorn Blade
For a sword that deals elemental damage, there are a couple of good choices. The Combuster, Glacius and Voltedge are a popular choice, and well-deserved of that popularity. The Divine Avenger is good if you like heavy, two-hit swords and last but not least, the Warmaster Rocket Hammer. Believe it or not, the Warmaster Rocket Hammer is actually the best choice in this lot but to be able to get it, you'll have to complete the tier 3 version of the expansion mission Operation Crimson Hammer, which costs real money. Alchemy paths:
Brandish - Fireburst/Iceburst/Shockburst Brandish - Blaze/Blizz/Bolt brand - Combuster/Glacius/Voltedge
Sealed Sword - Avenger - Divine Avenger
(Note: the Warmaster Rocket Hammer does have an alchemy path, but it's not craftable, as it can only be obtained by completing the expansion mission Operation Crimson Hammer)
Prototype Rocket Hammer - Stable Rocket Hammer - Warmaster Rocket Hammer
Guns/Bombs
As explained above, it is best to get a gun/bomb that deals normal damage, as they can be used in almost every situation. The best gun that deals normal damage would either be the Neutralizer (if you like slow-firing guns) or the Iron Slug. Here are their alchemy paths:
Catalyzer - Industrial Catalyzer - Volatile Catalyzer - Neutralizer
Magnus - Mega Magnus - Iron Slug
The best bomb that deals normal damage would either be the Nitronome (which has more speed) or the Big Angry Bomb (which has more power). In my opinion, I would choose the Nitronome because it isn't that much less powerful than the Big Angry Bomb but has significantly more speed. Alchemy paths:
Blast Bomb - Super Blast Bomb - Master Blast Bomb - Nitronome/Big Angry Bomb
As said above, please comment if you think that there should be changes made to this guide. And by the way, I've only posted half of this guide - I still haven't said anything about armors, helmets and shields yet - so would everyone like me to post the rest?
The Nitronome is an excellent weapon, but the guns you suggested really aren't great.
Neutralizer is for zombies (Biohazard outperforms it on nearly everything else) and Iron Slug is for slimes and constructs (which you really shouldn't even be using a Magnus on in the first place).