Preferred (or recommended) way to store large amounts of simulation configurations, runs values and final results
It sounds like you need to record more or less the same kinds of information for each case, so a relational database sounds like a good fit-- why do you think it's "not the proper way"? 
If your data fits in a collection of CSV files, you're most of the way to a relational database already! Just store in database tables instead, and you have support for foreign keys and queries. If you go on to implement an object-oriented solution, you can initialize your objects from the database.
I am working with some network simulator. After making some extensions to it, I need to make a lot of different simulations and tests. I need to record:

simulation scenario configurations
values of some parameters (e.g. buffer sizes, signal qualities, position) per devices per time unit t
final results computed from those recorded values

Second data is needed to perform some visualization after simulation was performed (simple animation, showing some statistics over time).
I am using Python with matplotlib etc. for post-processing the data and for writing a proper app (now considering pyQt or Django, but this is not the topic of the question). Now I am wondering what would be the best way to store this data?
My first guess was to use XML files, but it can be too much overhead from the XML syntax (I mean, files can grow up to very big sizes, especially for the second part of the data type). So I tried to design a database... But this also seems to me to be not the proper way... Maybe a mix of both?
I have tried to find some clues in Google, but found nothing special. Have you ever had a need for storing such data? How have you done that? Is there any "design pattern" for that?