There is still an entry for Gate of Thunder in TurboGrafx-16, other than that, everything looks good!

I finally got around to looking at the JP PC Engine section. Here's my list:

1941: Counter Attack - SuperGrafx title incompatible with standard systems; change name to: 1941: Counter Attack [SuperGrafx]
Aldynes - SuperGrafx title incompatible with standard systems; change name to: Aldynes [SuperGrafx]
Battle Ace - SuperGrafx title incompatible with standard systems; change name to: Battle Ace [SuperGrafx]
Bishoujo Senshi Sailor Moon Collection - CD game; move to: JP PC Engine CD
Castlevania: Rondo Of Blood - CD game that already has entry; delete entry
Cosmic Fantasy 2 - CD game; move to: JP PC Engine CD
Cyber City Oedo 808 - CD game; move to: JP PC Engine CD
Daimakaimura - SuperGrafx title incompatible with standard systems; change name to: Daimakaimura [SuperGrafx]
FX-Unit Yuki: The Henshin Engine - American CD homebrew; move to: TurboGrafx CD, change name to: FX-Unit Yuki: The Henshin Engine [Homebrew]
Finall Match Tennis - title misspelled; change name to: Final Match Tennis
Ginga Fukei Densetsu - CD game with inaccurate title; move to: JP PC Engine CD, change name to: Ginga Fukei Densetsu: Sapphire
Legend Of Xanadu - CD game; move to: JP PC Engine CD
Legend Of The Peach Boy - inaccurate title; change name to: Momotaro Densetsu Turbo
Mad Stalker [Turbo CD] - CD game with inaccurate title; move to: JP PC Engine CD, change name to: Mad Stalker
Magicoal - CD game; move to: JP PC Engine CD
PC Engine CD-ROM - CD system; move to: JP PC Engine CD
PC Engine CD-ROM Interface Unit - CD accessory; move to: JP PC Engine CD
PC Engire Duo-RX - misspelled title; change name to: PC Engine Duo-RX
Princess Maker - CD game; move to: JP PC Engine CD
Princess Maker 2 - CD game; move to: JP PC Engine CD
Rayxanber II - CD game; move to: JP PC Engine CD
Road Spirits - CD game; move to: JP PC Engine CD
Sotsuyo Graduation - CD game; move to: JP PC Engine CD
Star Parodier - CD game; move to: JP PC Engine CD
Super Graphx - misspelled title; change name to: SuperGrafx
The Legend Of Xanadu 2 - CD Game with inconsistent name; move to JP PC Engine CD, change name to: Legend Of Xanadu 2
Turbo DUO-R Controller - incorrect name; change name to: PC Engine Duo-R Controller
Turbo Pad Controller PI-D6 - incorrect name; change name to: Controller PI-D6
Turbo Pad Controller PI-PD002 - incorrect name; change name to: Controller PI-PD002
Turbo Pad Controller PI-PD8 - incorrect name; change name to: Controller PI-PD8
Turbo Pad Controller PI-TG8 - incorrect name; change name to: Controller PI-TG8
Valis III - CD game; move to: JP PC Engine CD
Valis: The Fantasm Soldier - CD game; move to: JP PC Engine CD
Winds Of Thunder - CD game that already has entry; delete entry
Youkai Douchuuki - duplicate entry; delete entry
Ys IV: The Dawn Of Ys - CD game; move to: JP PC Engine CD

Here's a list of issues from the TurboGrafx-16 section:

Atlantean - Homebrew title; change name to: Atlantean [Homebrew]
Darius Alpha [Japan] - Japanese release; move to: JP PC Engine
Gate of Thunder - Japanese CD release that already has entry in appropriate section; delete entry
Gate of Thunder, Bonk's Adventure, Bonk's Revenge - CD game; move to: TurboGrafx CD
Implode [Homebrew] - CD game; move to: TurboGrafx CD
Loom [CD] - CD game; move to: TurboGrafx CD
Magical Dinosaur Tour - CD game; move to: TurboGrafx CD
Snatcher - Japanese CD game; move to: JP PC Engine CD
Super System Card Ver.3.0 - Peripheral for CD games; move to: TurboGrafx CD
The Local Girls of Hawaii - CD game; move to: TurboGrafx CD
Toilet Kids [Japan] - Japanese game; move to: JP PC Engine
Turbo Duo R - not an actual release (Duo R was never released in America); delete entry
TurboGrafx-16 CD System - move to: TurboGrafx CD

I see no issues in the TurboGrafx CD section right now. Let me know when the changes are made, and I will then take a look at the JP PC Engine sections.

I do have contributor privileges, but I'm not quite sure how to do certain things. I seem unable to edit the names of games or to change what system they are for, which would be a big help in organizing the sections.

I would be delighted! TurboGrafx is one of my favorite systems and I would be honored to have the opportunity to help with that section of the site.