What should I be aware of when hiring a car from one of the cheaper rental firms in Spain?

This is a good question and here are some potential explanations :

1. Structure costs are lower for smaller firms so they can offer better prices. Bigger firms spend a lot of money on advertising and marketing.
2. Cars offered might be different : options available, number of kilometers, etc...
3. Services offered might be different : some will ask you to clean up or refuel the car before return. So you do a part of the car rental company job and you pay less.
4. Smaller firms usually don't offer any loyalty program and again you pay for this in bigger firms.
5. Smaller firms need to have a competitive advantage so they will cut down on their margin as the price is one aspect where they can make a difference. Bigger firms will attract more loyal customers, people looking for a well known brand rather than just a price.
6. The terms and conditions can be different : can you cancel your car rental? can you modify it? will there be a fee for these changes?
7. Insurance : this is a big part of the price and it is so complex with car rental that you can easily think that you have a good coverage while indeed you just got the basics.
8. Level of assistance : what support do you get if the car is damaged? will they provide you a new car? within which timeframe? does this also apply for flat tire? even if you are responsible for the damage? do they pay for the extra costs if they can't provide timely assistance?

As you can see, there are so many parameters to evaluate that can influence the price a lot.

I hired from an independent company (see also yelp page) in Ronda, Andalucía, Spain. I wrote a review detailing my experiences on Yelp but it appears that since I wrote it, the original company entry was deleted and a new one created, as there are now no reviews, just like when I decided to rent with that company. I don't remember if they were cheap but they were the only one I could find in Ronda, Spain (most car rentals are at airports but we arrived by train) as it had a Yelp listing and was mentioned on the tourist office website. After I arrived I saw ads (in the street) for others that did not have even that. This company was and is not listed on any car rental comparison site such as kayak.

The owner personally picked us up from the train station. Payment was cash only. He was friendly and handed over the car. I believe it is usually a car he lends out to loyal customers of his garage. It was old but it appeared functional to my untrained eyes, and anyway we were not really in a position to decline as we needed a car to get to our rural accommodation.

The car we received was bad. The gears were bad all the time (struggling uphill even in low gear) and two days before the end of our vacation, the gearbox broke completely and we were stuck in a rather remote place. I have never had this with a major rental company. We phoned the owner and I explained in the best Spanish I could that our gearbox was broken. An hour and a bit later (in the dark), he and his children arrived in his own car. When he was unable to fix the car on the spot, his children stayed with the rental car and he personally brought us to our residence (he drove the wrong way twice on the way). He did not offer us another car, and offered us a choice: either he could refund us for the final two days during which we would have no access to a car, or pick us up at 7:00, but that he would not pick us up if we opted for the refund. We opted for the pickup and two days later he was there at 7:00 as agreed, as we had to catch a train at 9:00.

This was the first and so far last and only time I have rented from a small independent company. Although he did not try to rip us off and did what he could after the car broke down (I don't believe he had another car), needless to say I was not entirely satisfied. I would recommend to stick with companies that are listed on websites that compare car rental companies. Note that this company is significantly smaller than the local Andalucían chains that exist at the major airports, that I have used several times with no problems.

The report by @gerrit is indeed something that you will less likely encounter with a big rental company as the have internal quality assurance and if one of their rental stations goes wild you can at least complain to the head quarters.

However in reality many independent small companies will get you a car which is just a new and in good shape as the big ones. From my experience though the cheap offers usually have some hooks somewhere. E.g. typically:

• You can only book empty-to-empty (you get a car with empty tank, but you can also return it empty) or even full-to-empty (you get a car with full tank and may return it empty) fuel options. It is very hard to estimate your fuel consumption accurately and actually return the car empty. Instead you loose money on the unused fuel which won't be refunded. Even worse in case of the full-to-empty option you are forced to buy one tank at the company's price which is oftentimes highly exaggerated.
• While the big ones typically have their office right at the airport/train station/... and have their cars parked in a parking lot in easy walking reach the cheap companies often have their offices and cars in a remote location. They usually offer you a free shuttle service from the airport, but this will of course cost some time.
• The independent companies oftentimes have a bad service. It is not unheard of that you need to wait an hour or two in line at their check-out office.
• Oftentimes these companies (that need to somehow make money after all) will try to talk you into insurances or optional services that you do not want. While big rental car companies have found out that asking people for extra options is a good income as well, they in my experience will accept a single "no, not needed" just like that without arguing, while some of the smaller companies tend to try you more, which will cause the faint hearted to finally accept things they do not want.

That said, you can also have a great experience with small companies. As far as I have seen the cars were always in good shape. If you are the type of person that arrives at their airport in a tired shape and you just want to get to your hotel fast, or you are the type of person that likes to get into pitfalls (such as not inspecting the form that you are signing close enough or accepting things you don't need) or you are the type of person that can get talked into thing, then I do not recommand this type of rental company. However if you are on a budget, you are OK with extra wait times and navigating around pitfalls then you can also get very good deals with the small companies.

(As a side note: You will oftentimes find much better rates even at the big companies if you do not book on their website directly, but rather at a broker. Sine you are German: In my experience e.g. the rate of the ADAC Autovermietung are usually quite good (and they work with big rental companies), although for most of their rates you must be a member).

One way that they save money is to be in a much cheaper location than the major chains.

I've rented from a local independent that was in a field a few miles from the airport (literally, they'd bought a field from a farmer, gravelled it over and put in a portakabin as their office). They had a minibus that ran from the airport to their location, but you had to know it exists, to find it at a busy airport, and to allow extra time for waiting for the bus.