The standard opinion given out nowadays is that they were used for storing foodstuffs but there are in fact several theories competing equally in the archaeological community including, cough, ritual. Plus they shade off into wells and settlements at the edges. Also there appear to be two types according to when they were built.
The later kind found in regions such as Ireland and (IIRC) the Western Isles tend to date from Viking to mediaeval times. These seem to be more obviously defensive, many being built into places such as streambanks and cliff-faces (though you could argue that these places also tend to be nice and cool, by water and/or wind, and hence suited to becoming storehouses also).
As to the earlier kind they would appear like burnt mounds to have had several uses, not always exclusive, and have been built both from and into other structures [I wonder if some originally stood alone before later incorporation, and think this applies even more probably to 'wells'].
Though this is a weekend, and a Bank Holiday one at that, I expect others here will bring their minds to bear on this subject - that's my excuse anyway.

[Being as 'ow no-one else has replied on the subject]
Marked on old Orcadian maps as erd-houses, not all earthhouses are strictly souterrain as a few are known to have originally had their roofs poking above ground level. They [usually] end in one or more chambers after a passage that may be short and sweet or tens of metres long. The passages are usually curved and generally seem to have had flat tops, but the chamber roofs are often corbelled and tend to be supported on several stone pillars. Construction materials vary from plain clay-lined to flags and/or thick slabs.
Often they are found within Broch Age structures. A few have been built into tombs or incorporated early material such as rock art. Indeed earthhouses and tombs have been confused, more especially the two-storeyed versions with the Taversoe Tuick type tomb (chambered cairns can turn out to be either it seems) - several human skulls were found within the Rennibister souterrain for instance. One reported fulgarite (a lighting blast into the ground) cuould have been a simple earthhouse, as the passage was through the wrong material and far too long for one of those.
Earthhouses have been found together with crude idols, stones with roughly marked necks. Some have had circular pits found in close proximity - I believe a few isolated examples of such pits have also been put under the category of 'mattie hole' and assigned to illegal distillers.
I speak of Orcadian examples in these matters.