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Ordinary, English scarecrows have been animated at least twice by aliens to flush out a Doctor hidden on Earth. They were animated by the Time Lords in order to find the Second Doctor in exile on Earth. Later, they were controlled by the Family of Blood and used to pressure the Tenth Doctor to come out of hiding.
The Second Doctor
According to at least one source, the two parts of his sentence at the end of The War Games were not carried out simultaneously. He was sent to begin his exile on Earth a significant period of time before he was forced to undergo regeneration. During this time he lived on Earth in the Carlton Grange Hotel, and generally enjoyed a relatively luxurious life of considerable fame.
One night, while appearing on the game show, Explain My Mystery, the Doctor was asked to consider the case of the farmer with the walking scarecrows. He wasn't able to do so. Thus, he arranged for an off-camera visit to the farm. When he arrived, the scarecrows duly began to walk around. Eventually, they captured him and revealed that they had been animated by the Time Lords in order to carry out the remaining part of his sentence. They then took him back to the TARDIS and forced him to regeneration. While he was undergoing his metamorphosis, they set the TARDIS to dematerialize, and quickly left, thus setting up the opening moments of the Third Doctor's existence.
The Tenth Doctor
Ordinary English scarecrows were tools used by the Family of Blood. They kidnapped Humans and took them to their spaceship to be used as bodies for the incorporeal Family. They were also used as an army to attack a boys school in 1913, where many were shot down. Eventually, they re-animated to do more of the Family's bidding. They were again inanimate after the family's defeat. Son of Mine was placed in suspended animation inside one of the scarecrows.
Abilities
Neither of the two groups of scarecrow were either living creatures or cybernetic in any way. They were both just ordinary scarecrows made of burlap and straw. Both groups were animated by an outside force. The distinction between the two can be said to be their relative abilities. The ones encountered by the Second Doctor could talk, induce regeneration in a Time Lord, and skillfully use a TARDIS console.
The ones encountered by the Tenth Doctor did not have the ability to speak, nor any apparent skill with electronics. They were simple servants, bound to do whatever their masters required.
Both groups were used as tools of convenience by their hidden masters. There is no indication that either the Time Lords or the Family of Blood use scarecrows on a regular basis, or, really, on any other occasion but the ones depicted.