Here's what I know of:
WDW
Monorail - They have released about 10 colors by now I think and two different versions the newer one has opening doors
Straight Track - pack of 4
Curved Track - pack of 4
Contemporary Hotel
Spaceship Earth (Discontinued) - This is the original one that the monorail went underneath spaceship earth.
Disneyana "Silver" Monorail - Very limited edition special packaging and the whole thing is colored silver
Disneyana "Silver" Contemporary - Same as above
Disneyana "Silver" Spaceship Earth - Same as above
TTC Switching Station (Discontinued) - Has three switches at each end to create three separate loops themed to TTC
Polynesian Hotel (Dicontinued) - Includes a great ceremonial house and station (If you by two of these and put the station parts end to end it creates a station that is the correct length of the train)
Grand Floridian Hotel (Discontinued) - The grand Floridian station
Cinderella Castle Playset
WDW Sign Set (Discontinued) - includes WDW Main Entrance sign(lights up), WDW directional road sign, Contemporary sign, Polynesian sign, and Grand Floridian sign(lights up)
WDW Tree and Light set (Discontinued) - Includes Main Street Light(lights up), tomorrowland metallic palm tree, and Contemporary "Dixie Cup" style tree
Astro Orbiter Attracion (Dicontinued) - Includes two disney characters and can be activated by the monorail with seperately sold attraction connector
Dumbo Attracion (Dicontinued) - Includes two disney characters and can be activated by the monorail with seperately sold attraction connector
Tea Cup Attracion (Dicontinued) - Includes two disney characters and can be activated by the monorail with seperately sold attraction connector
Attraction Connector (Dicontinued) - Plugs into attraction and attaches to monorail pylon
WDW Haunted Mansion (Discontinued) - No attraction connection
New Spaceship Earth - More of a standalone playset
Tree of Life Playset (Discontinued) - Really has nothing to do with monorail but is packaged in monorail packaging
Disneyland
Disneyland Monorail (Discontinued) - An accurate model of the Mark V monorail, this was the most detailed monorail two right down to the doors, rearview mirrors, and escape hatches and includes the Golden Gate Bridge
Disneyland Mini Monorail (Discontinued) - Same as above but only included the two end cars, a little less track, and no bridge
DCA Orange Stinger (Discontinued) - Works with attraction connector
DCA Golden Zephyr (Discontinued) - Works with attraction connector
DCA King Tritons Carousel (Discontinued) - Works with attraction connector
DCA California Screamin (Discontinued) - A real pain to put together but really big once its done with either orange or purple cars
WDW Monorail sold as Disneyland monorail - Just a different package for the WDW one
Disneyland Haunted Mansion (Discontinued) - Same as WDW version but modeled after Disneyland's Haunted Mansion
I think that covers most of it, I probably left something out or got something wrong so feel free to offer any correction.