Basically, you want to add metadata to the text. There are two basic ways to do this: 1) add the tags as text inline with the original text, 2) use a secondary file format that (XML, SQL, etc) that will hold information about the tags and to which sections they attach.

1. Inline text tags
This is what dellis (above) is describing. You add tags (usually marked with a special character to distinguish them from regular occurrences of the word) just before or just after the section that they describe. Also you can mark sections off from each other.
e.g.

----- [this line signals a new note]
&scalia &dissent &tort

[your notes here]

-----

In this way, you can use any number of tools to write and then process/search your notes. However, you're probably going to end up "getting your hands dirty" by having to hack together a system -- meaning deciding your syntax, determining which tools are useful (including some more "advanced" search tools). But in the end, it will be a system that fits your workflow and will a be completely open file format.

Here's another 43folders post that could give you some ideas:
http://tinyurl.com/23axgc

2. Tagging with Note software
Any number of current notebook apps will allow you to make separate notes and then add keyword tags to them. Off the top of my head (and without verifying their current functionality), I would say:

Mori
Tinderbox
Together
Scrivener
CP Notebook
Journler
Any number of wiki implementations (try TiddlyWiki)

The advantages of this approach are: less futzing around with the system, improvements that come for "free" (meaning that you don't have to implement them yourself), nicer interfaces. (all at the cost of having less control over the format and the system itself.)