In this blog I've added all officially confirmed Capital ships (military and civilian types), Shuttles, Civilian Ships and Transports from the movies. In fact all ships that are no starfighters / escape pods. If you know any more, please let me know!

SAGA
AA-9 Coruscant Freighter / Botajef Freighter Liner - Corellian Engineering - Ep II
Acclamator-class Republic Assalut Ship - Rothana Heavy Engineering - Ep II
Action VI Transport - Corellian Engineering - Ep II
C-9979 Landing Ship - Haor Chall Engineering - Ep I III
Consular-class Republic Space Cruiser - Corellian Engineering - Ep I
Corellian Starshuttle - Corellian Engineering - Ep I
CR-90 Corellian Corvette 'Blockade Runner' - Corellian Engineering - Ep.III IV VI
Diamond-class Commerce Guild Starship - Commerce Guild - Ep II
Braha'tok-class Gunship - Dornean Braha'ket Fleetworks Conglomerate - Ep VI
Dowager Queen (class unknown) - Unknown - Ep IV
Executor-class Star Destroyer - Kuat Drive Yards - Ep V VI
Firespray-class Patrol & Attack Ship - Kuat Systems Engineering - Ep II V
Giga-class Transport - Unknown - Ep II
Gozanti Cruiser - Unknown - Ep I II
GR-45 Medium Transport - Gallofree Yards - Ep IV
GR-75 Medium Transport - Gallofree Yards - Ep V VI
HAET-221 (High Altitude Entry Transport) - Mekuun - Ep III
Hardcell-class Techno Union Interstellar Transport - Techno Union - Ep II
Imperial I-class Star Destroyer - Kuat Drive Yards - Ep IV (*)
Imperial II-class Star Destroyer - Kuat Drive Yards - Ep V VI (*)
Lambda-class T4-a Shuttle - Sienar Fleet Systems (& Cygnus Spaceworks) - Ep V VI
Lucrehulk-class 3210 Battleship - Hoersch Kessel Drive - Ep I II III
Lucrehulk-class 3210 Droid Control Ship - Hoersch Kessel Drive - Ep I
Lucrehulk-Class LH-1740 Modular Control Core - Baktoid Armor Workshop - Ep I II III
MC80 Mon Calamari Cruiser (different models) - Mon Cal Shipyards - Ep VI
Munificent-class Star Frigate - Hoersch-Kessel Drive Inc. & Gwori Revolutionary Industries - Ep III
Naboo Royal Cruiser J-Type Diplomatic Barge - Theed Palace Space Vessel Engineering Corps - Ep II
Naboo Royal Starship J-Type 327 - Nubian Design Collective & Theed Palace Space Vessel Engineering Corps - Ep I
Naboo Star Skiff - Theed Palace Space Vessel Engineering Corps - Ep III
Naboo Yacht H-Type - Theed Palace Space Vessel Engineering Corps - Ep II
Nebulon B EF76 Escort Frigate - Kuat Drive Yards - Ep V VI
Providence-class Carrier / Destroyer - Free Dac Volunteers - Ep III
Punworcca 116-class Insterstellar Sloop (Solar Sailer) - Huppla Pasa Tisc Shipwrights Collective - Ep II
Recusant-class Light Destroyer - Hoersch-Kessel Drive Inc. & Free Dac Volunteers Engineering Corps - Ep III
Sentinel-class Landing Craft - Sienar Fleet Systems & Cygnus Spaceworks - Ep IV
Sheatipede-class Neimoidian Shuttle - Haor Chall Engineering - Ep I II III
Star Courier Prototype (Sith Infiltrator) - Republic Sienar Systems - Ep I
Taylander Shuttle - Unknown - Ep II
Theta-class T-2c Shuttle - Cygnus Spaceworks - Ep III
TIE Shuttle - Sienar Fleet Systems - Ep V
Venator-class Star Destroyer - Kuat Drive Yards - Ep III
YT-1300 Stock Light Freighter - Corellian Engineering - Ep II III IV V VI
YT-2400 Stock Light Freighter - Corellian Engineering - Ep IV

Unknown Capital Ships at the end of 'TESB' with the Rebel Fleet
Unknown mysterious Alliance ship at Battle for Endor
Unknown Alliance Vessels at Battle for Endor?
Unknown Shuttle used by Chancellor Valorum
Unknown Ships on Coruscant (many!)
Unknown ship at the outskirts of Mos Espa (now in WTS)
Tector-class Star Destroyer - Kuat Drive Yards - Ep VI? (**)

Spin-offs
Blackhawk Destroyer - Unknown - Droids Animated Series
CR20 Republic Troop Carrier - Corellian Engineering - Clone Wars Animated
'Demolisher' (unknown type) - Kuat Drive Yards (?) - Droids Animated Series
IBC Capital Ship - Unknown - Clone Wars Animated Series
Starrunner-class ship - Corellian Engineering - Droids Animated Series
StarSpeeder 3000 - Unknown - Star Tours
Towani Space Cruiser - Unknown - CoC / BfE
Trigon One - Custom Annoo-dat - Droids Animated Series

(*) Also indicated as Imperator-class
(**) Rumoured to appear in 'RotJ'