Forgot one: Norwood Crossing on the Robin Hood line between Langwith WT and Creswell!
Here's what I make to be the current list of gate boxes. Note however that not all of these are manually worked gates, many of these will be barrier crossings. There are also plenty of signal boxes with crossings attached.
EASTERN REGION
Carlton
Claypole
Finningley
Grassthorpe Lane
Helpston
Ranskill
Woodcroft
Brundall (works in conjunction with adjacent signal box)
Chapel Road
Elsenham
Foxton
Ingatestone
Lincoln Road
Lingwood
Stowmarket
Strumpshaw
Trinity Marsh Lane
Whittlesea (works in conjunction with adjacent signal box)
Deep Wharf Crossing
Jurgens Crossing
Thames Board Mills Crossing
Barrow Road Crossing
Bonsall Lane
Godnow Bridge
Medge Hall
LONDON MIDLAND REGION
Burneside Higher
Fine Lane
Littons Mill Crossing
Llanfair PG
Norbury Hollow Crossing
Roddige
Tal-y-cafn
Ty-croes
Hilton Crossing (works in conjunction with adjacent signal box)
Cheltenham Alstone
Norwood Crossing
Wyfordby
Wymondham
Chapel Lane
Crofton
Norton
Red Lane
Kirksanton
Limestone Hall
Saltcoats
Skelly Crag
NORTH EASTERN REGION
Barlby
Bedale
Belmont
Cave Crossing
Common Road
Denton Village
Dormer Green
Green Oak Goit
Gristhorpe
Hammerton Road
Hessay
Hirst Lane
Howsham
Lane Head
Lebberston Road
Marston Moor
Milton Village
Noblethorpe
North Seaton
Oxmardyke
Spittal
Urlay Nook
Welton
Whixley
Wilstrop
SOUTHERN REGION
Charlton Lane Crossing
Chartham
Grain Crossing
Whyteleafe South
Wye
School Road
WESTERN REGION
Bishton Crossing
Colthrop Crossing
Kintbury Crossing
Pantyffynnon
Puxton & Worle
Red Cow (supervises only)
St Mary's Crossing
Llwyn Cadwgan (supervises only)