
Major thanks to @Oneye @Your Destiny and @Guy for providing benchmark (usually AI piloted) of effective designs to measure my own ships against. Further thanks to @Equalizer for sharing his ion layout and @Jenwuf for Ion Concentrator/Converger inspiration.
Legend regarding designation tags:[spoiler]Ships are categorized & classified by cost bracket.
Sub-500k Assault Craft; [LAC] & [HAC] for Light/Heavy variations
500k-750k Frigates, [FF]
750k-1m Destroyers, [DD]
==========
Above 1m are Capital Ships
1.25m-2.5m Cruisers; [CL] / [CR] / [CA] for Light/Standard/Heavy variations
2.5m-3.5m Battlecruisers, [BC]
3.5m-4.5m Battleships, [BB]
==========
Above 4.5m are Supercapital Ships
4.5m-6.5m Dreadnoughts, [DN]
6.5m+ Superdreadnoughts, [SD][/spoiler]
[SD] Crusader
6.791m Credits | 1,718 Crew | 8,035.6t Mass
Highest Difficulty Passed: Oneeye's Supremacy Mk2

CQB Missile/Ion boat, using overthrust to prevent itself from being railfanned. Derived from a pure missile carrier with heavily armored/shielded central citadel (to absorb railgun rounds), testing showed cutting channels for ion beams decreased survivability by perhaps 10% whilst non-trivially increasing drill rate.
Instructions:
This is a CQB optimized ship/"Hugger". When engaging in combat, use X to overthrust through the opponent (after right clicking/waiting to ensure proper alignment) then right-click onto the opponent as contact is made.
To ensure proper Flak Pod deployment, do not issue movement commands until after releasing Flak Pods and turning on their thrusters.
Commands:
Select all subships before issuing hotkey commands!
Press 0 to release Side Flak Pods.
Press 1 to deploy captive sub-ships. Note: some Spinning (deselect side pods, press R to turn the main ship) may be require be required to fully deploy Side Flak Pods.
Press 2 to select central Ion Beams
Press 3 to select external EMP missiles
Press 4 to select Port Missile batteries
Press 5 to select Starboard Missile batteries
Press 6 to select central Missile well
Vulnerabilities:
-Entire missile tower (>45% ship's firepower!) could be detached with detonation of 4th internal missile bay's second missile factory. Both sides.
-Serious protection on frontal aspect only.
-Completely vulnerable rear aspect.
-Can take significant damage from being railfanned.
-Can be Railfanned before contact is made.
-Weak retrothrust, but retreat is for cowards anyways!
Variants:
None
[DN] Raze MkII
4.687m Credits | 660 Crew | 7946.0t Mass
Highest Difficulty Passed: Your Destiny's The Beast

CQB Ion Converger using overthrust to prevent itself from being railfanned. Concentrating 30 ions into a beam waist 25 blocks wide, the Raze proceeds to "hug" the target and erase anything at the point of contact with (as of Patch 0.14.7_RC4) 75,000 DPS, with a damage density of 3000 damage per block per second along the point of contact.
Instructions:
This is a CQB optimized ship/"Hugger". When engaging in combat, use X to overthrust through the opponent (after right clicking/waiting to ensure proper alignment) then right-click onto the opponent as contact is made.
To ensure proper Flak Pod deployment, do not issue movement commands until after releasing Flak Pods and turning on their thrusters.
Commands:
Select all subships before issuing hotkey commands!
Press 0 to release Side Flak Pods and Beam Convergence System.
Press 1 to deploy captive sub-ships. Note: some Spinning (deselect side pods, press R to turn the main ship) may be require be required to fully deploy Side Flak Pods.
Use Boost Thrusters to maintain Beam Convergence / ensure side beam pods stay locked into position. The Raze MkII can indefinitely maintain beam subpod boost!
Press 8 to select Ion Beams
Vulnerabilities:
-No missiles - vulnerable to chunks of enemy ship shooting you as they fall off!
-Serious protection on frontal aspect only.
-Completely vulnerable rear aspect.
-Fragile side beam systems.
-Can be Railfanned before contact is made.
-Weak retrothrust, but retreat is for cowards anyways!
Variants:
[DN] Raze MkIII Mod 0
5.062m Credits | 816 Crew | 8157.7t Mass

In development variant, increasing vulnerability to being railfanned and decreasing beam-pod lockup strength in exchange for installing a puny 8 missile launcher battery.
EDIT: Further modern ship classes [Wasp, Onslaught Equalizer, Phaeston, Radiance, Eradica to be posted pending write-ups]