Simpler is better. There are so many powerful free or cheap tools out there. I would recommend starting with them. If they don't fit your needs, then you can plunk down your money on something more specialized and expensive.

Through trial and error, I've developed a few basic principles regarding academic tools:

1) They should be cross-platform and/or platform independent (or allow for easy export to a cross-platform format). I was burned many times on this in the past, using proprietary Mac software (on the old classic Mac) that was highly difficult to extract for use either on Mac OS X or Windows. Besides, academics are highly mobile types--at least at the beginning of their careers--and you never know what type of computer environment you'll be working in. Sometimes you'll even have to pay for a file conversion utility. For this reason, I prefer not to use any software that locks me into a proprietary format.

2) They should be accessible 30 years from now. This is related to #1. I'm at the beginning of my career. But already, because of poor organization and poor choice of technology, I've lost access to many of the academic notes I took just a few years ago. I'm committed not to let this happen again. Hence, the plain text files (see below).

3) Hoarding sources does not substitute for reading and note-taking. There are many tools out there that will let you save, clip, digitize anything you come across. These are great if you have some convenient way to search and/or filter them when you're actually writing something (such as the Mac program DevonThink). More often than not, however, the result is a mountain of articles, clippings, sources that remain unread and are a source of stress. Even if you collect broadly, you still have to set up practices of reading deeply.

4) Find media and/or programs that fit the logic of your own work-style. For instance, I've always been someone who has a hundred random thoughts firing in my mind. Index cards have helped me corral some of these and thus reduce the stress caused when I tried to hang on to all of them in my mind.

5) Give yourself the freedom of doodling, free-writing, etc. Legal pads and cheap notebooks are great for this. Sometimes, you simply have to work an idea over and over again until it works--i.e., until you're ready to commit it to writing.

So here are my tools:

For note taking, index cards and legal pads.

For electronic storage (i.e., the end repository of the notes I take by hand and then type into the computer), plain text files.

Plain text files are great because you can search them using grep, which will pull up any line that contains a certain word/character pattern. If you want to get all fancy, you can add tags and fields (see this here.)

(An aside: taking notes by hand and then typing them into the computer has completely revolutionized my academic research. By going over the notes twice, I now remember almost everything I read. Handwriting etches the note in my brain--retyping forces me to review it--and the electronic database format makes it instantly accessible again.)

For outlining, VIM outliner. Fantastically fast and simple to use.

For drafting, a plain text file. I would strongly recommend drafting your articles in something other than a Word Processor (be it legal pads or a text editor). This will draw a boundary between drafting and polishing. (When I drafted in Word, the WYSIWYG format sometimes paralyzed me, making me think my prose had to be perfect the first time through.)

After I've finished a draft, either Word or LaTeX for formatting. (Many editors in the humanities will only accept things in Word.)