Aliens living among us could be enemies of the invaders.

Atlantis...maybe the ancients were advanced and they were wiped out in a previous war but now the invaders had found out that we survived....and so did the Atlanteans.

One of their lost ships was found and captured by us and we have a significant person or person to their culture.

They're looking for a lost relic taken from them by yet another race and it was hidden here.

They were here first and some other race colonized Earth with us.

They were here first and left before the dinosaur killing meteor hit and we evolved from something left behind.

I guess that's it.
*Hazmat Suit Hugs*
Still sick...Bailey.

...but not a good reason to keep slaves.

Consider things outside the box when you talk about resources. Battle: Los Angeles is a prime example of this. They came for water. Yes, there are ide asteroids in the solar system, but we have a LOT of water, and a high tech race will have discovered how to purify salt water efficiently.

But, you may have noticed that I mention this is a horrible reason for them to enslave the populace. If the resource is abundant enough on the planet for them to come, then they just ignore the population, by and large, as they take it.

In my opinion, the end of Battle: Los Angeles is a humanocentric cop out. Sure, it was nice to have a melancholy ending where a sad one was almost guaranteed, but the alien race should probably have won.

Ok, on to my ideas...

They are an "uplift" race. They feel that races must be properly brought into the galactic community. Properly means that the race must be conditioned to look at the universe the way that they do, whatever that us. As such, they find races about ready to join the galactic community and 'enroll them in school.'

They are human. Maybe not what you're looking for, but what if the race is human, and have been looking for earth for thousands of years. Similar to the Atlantis idea, and possibly linked to it, but humanity shed the chains of earth before a calamity destroyed much of the technology that was here. They're back looking for the homeworld of legend. When they find it inhabited, they enslave those that remained because they want the planet for themselves. It's their birthright after all.

Like the billions of unique genes in our biosphere.

We are (will be) not advanced enough to take advantage of them and we don't really have the need. Our biosphere works well or used to and could again if we decrease greenhouse gases in our atmosphere and do a lot more to protect all species; completely stop the reduction of biodiversity.

Maybe the aliens are very good at physical, mechanical, electronic, etc. technology, but they aren't good at biology. Long ago they might have eliminated their own biosphere and just turn raw materials into food or whatever. Now they are intelligent enough to grasp biology, but have very little to work with. All genes from bacteria to trees and people have had long evolution to make very subtle, beautiful solutions to countless physical/chemical problems. Bacteria species can live in a very wide variety of environments, use all kinds of things for food, excrete all kinds of materials/chemicals and breakdown many chemicals that are toxic for most other kinds of life. Plants can't "run away" from their predators, so make amazing chemicals to fight off animals, fungi, bacteria, viruses, etc. Animals physically solve very many problems and create eagle eyes, humyn brains and all other sorts of wonderful apparatus. (apparati ?)

These genetic resources could solve all sorts of problems like terra-forming planets, fighting plagues or invasive species from other planets the aliens have encountered, but don't know enough bio to effectively deal with.

I remember a sci-fi story where Earth tech was not advanced compared to other races, but we were best by far at biology and medicine; it was the one thing humyns could trade for alien tech.

...this hasn't been mentioned yet, but there's also the idea of interstellar refugees.

A year or two back there was a particularly badly done series on, I think, either CBS or NBC about a group of aliens that looked, oddly enough, almost exactly like humans, but was distinguishable readily enough with simple blood tests. They had come to earth to scout out a potential refuge for their planet, which orbited a star on the verge of going nova. On arrival, most were captured and detained for decades in a secret base in Alaska.

Push came to shove, and due to a variety of poorly thought out factors, the aliens became rushed in having to get their homeworld evacuated, and Earth, of course, was the only habitable planet they'd been able to find. They determined that not only did humanity not have any capability to co-habitate planet, but that there were just too darn many of us, and so started doing very dumb and, again, not well-thought-out (by the characters or by the writers; very bad epidemiology is very, very bad) things to cull the current tenants (us). The show was (correctly, as it was a real stinker) canceled, so who knows whether or not they would have gotten all their population here, or whether the increasingly jingoistic government would have stopped them (or whether the very ambiguous protagonists would have taken a third way), but the premise holds: THEY want our planet because they are running from something, it's habitable, and, unfortunately for us, they have no compunctions about taking slaves.

tl;dr: Alien refugees take over.

I had a pretty cool idea. Some people say their best ideas come to them in the shower, mine are when I'm driving.

What if this alien race is adaptive biologically? They need to adapt or they begin to die out. Their Genome has a terminal flaw in that if they breed with their own race, then it actually homogenizes after a few generations and they would become susceptible to numerous genetic related ailments.

So, they have enslaved the humans as breeding stock.

On a related concept, an egg laying a-sexual race wants to use us as mobile incubators.