Differences between MSc Program in Engineering in TU and Research Universities in the Netherlands In the Netherlands what is the difference between universities of technology (TU's) and research universities? 

Also both universities of technology and of research offer engineering MSc programs. Is there a difference between them? Is one inferior to the other in any way?  Would it be better to study a MSc program in engineering in a university of technology?
Both type of universities are research intensive, so the adjective "research" is not useful to distinguish them. In the Netherlands they are usually called "classical" and "technical" universities, which is the terminology I will use here. In general the distinction is that the universities of technology are more application-oriented, while the other classical universities are more theory-oriented. The TU's typically have closer ties to industry. Of course in current research the boundary between "applied" and "theoretical" research is not always so clear, and you will find both types of research in both types of universities, but in general this is one of the main things that distinguish the universities.

Another difference is that the TU's also only offer programs in engineering and related disciplines (with a few exceptions), while the classical universities also offer courses in the humanities and social sciences.

What is better in terms of choosing a university to study depends on what your interests are. Most engineering programs (like civil engineering) are only offered at the TU's, but programs such as computer science, mathematics or physics are offered on both types of universities, although their focus will be different as explained above.

Apart from that, there are also "Hogescholen" which in English are typically called "University of Applied Sciences" or something similar. These types of institutions are not research-oriented and typically do not offer graduate programs (or only for MSc and not PhD).