In both the book, and the movie, the Fellowship sees a dark cloud approaching before Legolas's keen eyes see the cloud is really a flock of birds likely spying for Saruman and the Fellowship hides until they fly by. Considering an Elf could see them before they could see him, I have to wonder just how useful Saruman's avian spies really were. Are there other instances (beyond this flock and the Bard's thrush) where JRRT employed avian spies in middle-earth?
Thorondor and the other great eagles did a lot of spying in the Silmarillion. Radagast could also employ birds in this way.
Send out messages to all the beasts and birds that are your friends. Tell them to bring news of anything that bears on this matter to Saruman and Gandalf.
(The Council of Elrond)
Tolkien's Middle Earth contained a number of intelligent bird species, mostly those that had been exposed to high-level magic (or were Maia in disguise) rather than as a result of normal evolution.
The intelligent ravens of Ravenhill near Erebor, could live to a great age and some could even speak Westron.
They are reputedly the messengers of the Vala Mandos
Spirits in the shapes of hawks and eagles were the servants of Manwë Súlimo, continually flying over Middle-earth to gather information for their master. Above many flocks of crebain, Aragorn noticed hawks, flying high in the sky, during the War of the Ring.
The great Eagles are obviously to be considered, both in the first, second and third ages. There were also the Thrush's in dale that you mention. Gwaiwar is also made 'King of All the Birds' at the conclusion of The Hobbit.
On the opposing side the Crebain from Dunland and no dubt other places had a large part. Sauron also had vampire-bats trained to attack his enemies and one needs to wonder about Thuringwethil in that regard. He had such dominion over the creatures under his power for any length of time that they all began to change and show darker characteristics - even the 'Flies of Mordor' were marked with the symbol of his eye.