Some HO models I know of in recent years, with some repeats from what others have listed
Atlas
* C420
* S1, 415, 420
* H16-44
* RS-1
* RS-3
* Cabooses #1, #5
* GP38-2 (Trainman)
LifeLike
* GP38-2
Walthers
* Heavyweight 28-1 Parlor car with blue stripe - include decals with various names
* Baggage car - include decals with various numbers
* Alco FA-1
Con-Cor
* MP54 in three models, 12 unique numbers all together
True Line Trains
* C-Liner, in two color schemes, 4 numbers total
IHC
* Cannonball Parlors cars
* Heavyweights - orange stripe
Inter Mountain/Bethlehem Car Works
* Coach - three numbers
* I think they make a baggage car too
Stewart
* Baldwin DS 4-4-1000
New York & Atlantic
* Athearn blue box GP38-2
Division Point (brass)
* RS-2
* C-Liner
There are a number of resin kits too
Island Model Works -
http://www.islandmodelworks.com/ - lots of LIRR models
Funaro & Camerlengo -
http://www.fandckits.com/ - LIRR passenger, cabooses, gondola
Westerfield -
http://www.westerfield.biz/ - LIRR box cars