Fantasy Zone port list:

Arcade System 16 Original style:

- PCB Super Gun
¤The most nostalgic way.

- Sharp X68000
¤exclusive Space Harrier stage

- Sega Ages - Saturn
¤http://strategywiki.org/wiki/Fantasy_Zone/Secrets#Sega_Saturn

- Sega 2500 volume 3 - Fantasy Zone
¤PS2 enhanced: 4 brand new stages and brand new weapons.

- Sega 2500 volume 33 - Fantasy Zone Complete Collection
¤Supports rapid fire and an in-game time attack mode but I think it has less extras than Saturn, need to check and see.

- Xbox/PS3 - Sega Mega Drive complete collection/Sega Sonic Genesis Collection
¤Similar to above

- 3DS - Fantasy Zone: Opa-Opa Bros
¤Features rapid fire, Sega Master System exclusive bosses appear in System 16 form by default but becomes a dip switch once you've encountered the hidden Round 4 boss.

"Factory Default" is when you boot up the game and/or set the options back to default.
With or without Rapid Fire is based on the system you play it on and whether it is doable without using a 3rd Party Turbo Controller.
eg PCB Supergun (actual arcade) is no but PS2 via control options is yes.

For custom options it looks like Saturn wins by having the option to disable price inflation and infinite weapon time on a console.
PS2 enhanced feels like a Directors Cut making it a very different game
3DS Opa Opa Bros has 2 unique options:
Upa-upa mode or an Opa-Opa run with 2 SMS bosses taking over stages 4 and 6.

Sega 8-bit

- Original Console (Master System/Mark 3)
NTSC Consoles can use RGB SCART

- Wii Virtual Console (no Wii U eshop version yet)
¤Supports 240p, 480i, 480p and Rapid Fire.
NTSC Wii cannot use SCART so S-Video/Component

- PS2 Sega 2500 - Fantasy Zone Complete Collection
¤Supports 240p, 480i, 480p, Rapid Fire and faster loading times by setting High Clock speed to on.
I think SCART is supported.

Nintendo 8-Bit

- Famicom by Sunsoft

- NES by Tengen
A speed run has been done by Peaches

- "Neo Classic" via PS2 Sega 2500 volume 33 - Fantasy Zone Complete Collection.
Loosely based on Famicom version

Other lesser known ports goes here

MSX
MZ-700
Turbo-Grafx 16