Can a master's thesis still be good if it lacks demonstrable results? I am currently writing my master's thesis, but I have a sneaking suspicion that it will not be very good. This is partly because I have been unable to test the system I propose in the thesis properly, because testing it involves test cases that has to be manually performed, and I simply haven't got the time/resources/mental sanity to do more than a handful of them.

The problem is that having little testing could be viewed as a large, weak point in my thesis, and is easily attackable when I shall defend it.
My thesis is about detecting malware that requires human interaction (hence the testing difficulty), and by looking at some indicators I can determine what is malware and what is not. But my fear is that these results won't be very generalizable because of the small sample size. So my question is then: can a master thesis still be good if the presented results only cover a laughably small sample size?
My Masters project (synthetic chemistry) didn't actually generate results other than failure and black goop (so nothing novel!) until the last two weeks of time I had in the lab, and even then, there was insufficient purity and quantity of my compound to do a complete 'standard' panel of analysis. It was the 4th year of an integrated BSc/Msci course, was graded including a viva and I achieved a mid 2.1. 

The main purpose of a research Masters, at least in chemistry, is to accustom you to 'proper' research methods, while allowing you to pursue something novel and to demonstrate your ability to conduct research to a sufficient standard. In my cohort there was typically a tradeoff between novelty of project and quality of results, where one forgave the lack of the other.

As long as your thesis is written with an awareness of its deficits (aims far loftier/broader than the time/resources available sounds like a good start!) and you write good further work and conclusion sections where you tie this awareness in, making sensible conclusions and observations on the few cases you have achieved, I think it is definitely possible to write a good one! As Paul indicated above, you should discuss these concerns with your supervisor and possibly head of class (or equivalent). I am sure they will have dealt with someone with your concerns and circumstances before.