Content Management

Not really, it sounds like a database is more what you need. Content Management Systems are used primarily to manage content of websites, and by content we typically mean articles, blog posts and other lengthy text based data. I'm assuming your data doesn't necessarily have to be available via a website, and that a desktop application/s would suffice? In addition, I'm also assuming that you don't want to spend a large amount of time creating your own database tables and so forth, rather that you have an application that manages the data structures for you?

With that in mind, I see two possibilities:
1. Tree-Style note taking software (sometimes known as an "outline manager"
2. A PIM or Personal Information Manager, which is primarily meant for contact and appointment information but often features the ability to store notes.

For number there are several possibilities... As I mention in my first post, TiddlyWiki will do what you need it to do. It's a self-contained, self-modifying single HTML file that you edit (offline) in your browser. You can enter text in small chunks called tiddlers, titling and tagging them and all this text is searcheable. This is essentially a "personal Wiki" but the big advantage is that the structure is very free allowing you to determine exactly how you split up and categorize your data. WikiOnAStick is a similiar alternative to TiddlyWiki, likewise considered a portable personal Wiki (since it's a single HTML file all you need is a browser to edit the content).

As for tree-style note takers there are a number to choose from with one of the best I have seen being
KeyNote. The basic premise of a tree-style note taker is that you create a tree-like structure (think of folders like in Windows Explorer). Each node (folder) can have an associated parent and children nodes, and each of those nodes can contain notes. So for example, you might have a for one specific job, and under that node, you have 3 children nodes; "Drawing Issues", "Jobs" and "Correspondance". You can then put your notes in the relevent place. Naturally you can keep adding and nesting nodes depending on your needs (I hope this all makes sense!). Like I said, Keynote is one of the best of these type of tools that I've found, very detailed (but easy to use), with lots of features to help you organize information.

A simpler alternative to Keynote is Mempad, which doesn't contain all the bells and whistles, but the underlying principle is the same as Keynote.

A more complex (but perhaps more powerful) application is the more database-driven Neomem. I haven't really used this application so I can't give too much information about it except to say that it appear to be less intuitive than the other software mentioned above. Similarly, TreeLine is a more "hardcore" database-style notes organizer. I've used it a tiny bit, and it's very powerful but will definitely take some reading.

I'm not really familiar with many decent (and portable) PIM applications. The only one I've ever used is EssentialPIM. It seems to be good at what it does. As stated above the goal of a PIM is to bring together all your appointment and contact information with the added benefit of being able to store personal notes. I see from the EssentialPIM website that they have a "portable" edition, which is U3. I'd avoid this version as the U3 platform is essentially (no pun intended) dead. The free version of EP is also portable AFAIK.

All of the above programs are portable to the best of my knowledge and they are all free (or free versions are available). This means that you can try them out without any commitment. The most important thing, as I already mentioned is to find something that you're comfortable using. Make the software fit your system, don't try to alter your system (too significantly) to fit the software (unless your system is highly disorganized!). You must be comfortable with the software you're using otherwise it will hinder, not help you. Also keep in mind that perhaps you might have to use more than one program to do what you want to do, rather than try to force one program to fulfill all your needs.