I once had a teacher (believe this or not) say that there was such a thing as too much research. Initially I thought, "what rubbish," but now I can honestly say that when it comes to certain things, yes, there can be too much research. Research for it's own sake is good I think. Never stop learning and expanding your knowledge base are two things that I feel are important to a writer. What makes it into your story is where your inner editor kicks in. Just because you've learned all the lingo or terms for a particular occupation of a character, it doesn't mean that they should be used exclusively or at every opportunity. I've found that I personally can fall into the trap of using a word and simply assuming that others will know what I mean though context. I find things like that when I edit. It's especially true once I've been working with a particular work for a while and intensively. I get so into it, you know?
Then, of course, there are the many kinds of writing software. Some people still love to write by hand. Yes, I mean with a pen or pencil on paper. While that's fine I'm indefinitely faster at typing to get my thoughts out on paper. There are times that I just have to write on paper though. It's like an itch. There's something extremely gratifying about putting a pen to paper and feeling the ink glide across the paper. That being said, I'll turn back to the software issue. There are very popular applications such as Scrivner, Storyist, and yWriter that will contain pretty much any kind of research you want as well as your story-in-progress. I have fiddled with all three and I prefer yWriter. For me it's a blend of a desirable interface and the perfect price. It's free! There is no "right" or "wrong" way to organize research. It's all what works best for the individual.
I think that covers just about everything (and then some, I'm sure) of my thoughts on research. It's a rambling account so I apologize and hope that my two cents are worth something to someone out there!