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.