I primarily focus on collecting pyro models from the OT and have also spent a lot of time talking with crew members and ILM crew guys who worked on the prequels.
Of the prequels some miniature explosions were used in the final sequence in TPM however 90% of the shots in the final battle were CGI.
However in AOTC and ROTS the only miniatures that were made were essentially blank "bucks" used to composite the CG models for basic shape and then they were finished digitally.No miniature ship models were used in either AOTC or ROTS.
That is not to say that miniatures were not used.As has been shown there were sections of Theed built in miniature and the hangar.Parts of Kashykk and Mustafar and Utapau were made in miniature and also some parts of the Opera in ROTS.
As also noted Jar-Jar was not 100% CG.Along with the moment noted when you see Binks juggling in Watto's workshop that was also an actor in the suit.Of course these scenes were also touched up digitally in post but started with physical actors and props.There were also full-scale static Battle Droids made for all three prequels and used at various points.
The reason I am fascinated with miniatures is that they are,effects-wise,the one constant throughout the six films in one form or another.Obviously the hero sabers are also a constant however either A)they have been destroyed or B) are in the LFL archives or C) are in private hands and cost a small fortune which will always be beyond my reach.Miniatures,particularly ship models,represent and reflect a dying part of the VFX industry and are therefore,for me,an essential thing to preserve.