What is the inspiration for the Awaken spell (found at least in D&D 3.5e)? Why would a druid use it apart from enslaving creatures with intelligence and specialized forms? I'm thinking that it's "unnatural" for an animal or tree to have intelligence, so it seems to offend the druid's preference for what is natural. Does it come from some fiction that justifies it?
While it's certainly a niche spell you won't come across that often, it does have some uses.
Awaken works on plants as well as animals. If you have a favorite campsite, you could Awaken some trees around it to act as sentries and guards. This is not a particularly efficient use of XP, but would make some very neat flavor for a Druid's grove. It could also be used to scare off poachers of low level (like common townsfolk).
For animals, intelligent animals can be useful as spies. Nobody thinks twice about a cat going around town. A cat that can speak common would be a fairly useful scout in the home of someone you want to watch, especially if it's their cat. A few of them could cover a town and know what's going on.
In both cases, as the targets are sentient, you can befriend them. They start off friendly, but you could work to make them cohorts or allies the same as any other friendly NPC. This can let you do some interesting things.
Theoretically if a DM allowed it, another PC could actually play one of these as a character. That would be... different.
As Ellesedil mentioned in his comment, you could also use it to attack someone who is mistreating an animal companion by making that animal intelligent. It's now no longer their companion, and with it's intelligence it may harbor a grudge. (Note that this won't work on a familiar or Paladin mount, as both are treated as Magical Beasts.)
I suppose you could also ask your newly sentient animals to attack. Although the spell says they will serve you "in specific tasks or endeavors", they are sentient beings now and can't just be bossed around endlessly. So that is not very practical either.
You don't see PCs doing that very often because of the XP cost, but I can see a situation where NPCs could have a lot of fun with it.
Is it Evil?
I don't think using this spell is inherently evil. If you're using it to release an animal companion in the service of an evil Druid, that is not an evil act. Making an intelligent tree around a Druidic grove doesn't seem like an evil act.
If you're using Awaken on an animal so that you can experiment or torture something intelligent, that would be evil. I'd argue, however, that it's the evil act itself and not the awaken that makes it so.
As with a lot of spells it's possible to use it in an evil way, but I don't see anything overtly evil about this one. You could definitely make a case that it's not natural and that any given Druid might react negatively to other Druids using it. That would be perfectly legitimate character opinion, but that's essentially politics and not something for the alignment system.
Where did it come from?
I don't have a specific source that would justify that. The AD&D PHB had a spell called Animate Rock (alternate source). That works similarly to Awaken (actually like Animate Object), only on rocks, and was also available to Clerics. A likely explanation is that the 3.0 designers wanted to keep the spell but realized that doing it to rocks doesn't actually make a whole lot of sense for Druids, so when Druids got their own spell list they gave them a more Druidic themed version.
Magical Beasts (which include intelligent animals) are already in the game, however. There's also sentient plants like Treants, although the spell doesn't let you create those specifically. It seems like a better fit than animated rocks.
Why would it be unnatural? The druid’s magic is part of the nature of their world. Channeling some of that power into a creature is no more unnatural than bringing water to a field to help it grow. Sure, the water wouldn’t have gone there “naturally,” if by that you mean without the druid taking an active role in making it go there, but the druid himself is a natural creature.
The important thing is that awaken empowers the creature to be a better representative of its kind. It enhances the creature without twisting it, the way, perhaps, a transmuter (e.g. owlbear) or necromancer (e.g. undead) or even an angel (e.g. celestial creature) might.
Also, evil druids are still just as in favor of the “natural” as are good or neutral druids, they just use the power of nature to empower themselves, to the detriment of those around them.
Keep in mind that awaken doesn't actually give you much ability to control the target. For any target other than your most recent, the creature starts out friendly toward you and understands that you're responsible for its sentience, but after that moment, its attitude (and willingness to help) is no more under your control than anyone else's is. Your most recent target is essentially charmed, but that's not domination, and it only works on one target anyway. Either way, if you treat these creatures badly enough to lose their friendship -which is harder for your most recent target, owing to the charm-like effect, but still not impossible- they will leave.
Also, to add to the list of possible uses, imagine a pack of animals that is constantly being harassed by humanoids; it might even be subject to poaching. A druid might awaken the leader of such a pack, or several of its stronger members, so that they can better protect the pack.
For a truly fantastic example, consider the possibility that one of these stronger members eventually becomes a druid himself. This could result in a self-perpetuating society where all the mature packmates are awakened, and the druid awakens the young after reaching a certain age, eventually training a successor.
If you really want to get exotic, this might even form the basis for an interesting DMPC (or even a PC, if a player feels up to the challenge of playing a species without opposable thumbs). The pack has lost its only remaining druid, and has sent out one of its members to learn the ways of the class and, most importantly, the secret of awakening. If he fails, then the pack will revert to nonsentience as the awakened members die out.