I've been trying to get good pen picutres as well, and while my photos have improved quite a bit, I still have a long way to go.
That said, I'd list the basics as:
composition,
lighting, and
exposure.
The camera controls are the tools we use to achieve our basic goals. Unfortunately, those details are easier to discuss and often obscure the underlying principles they serve. I apologize for sounding preachy, but many of us (myself included) tend to get caught up in the mechanics of photography and fail to actually see what we're photographing in the first place.
One device that helps me surmount this problem is some software that allows me to control the camera directly from my computer. Once everything is set up, I press a key. The camera takes the picture and transfers it directly to an image editing program. I can immediately see a full-size result. Problems are much more evident, and I can easily compare multiple shots. This greatly sped up my experimentation and, quite frankly, I was surprised at some of the results. For example, I hadn't realized just how much of a difference a 1/3 f-stop change in exposure can really make. The camera's histogram had fooled me into thinking that I had a lot more leeway in exposure.
Good lighting is more difficult to achieve than correct exposure. I'm still playing with two lamps (although I may wish to add another, or perhaps a bounce flash). I've gone from using a light tent to going without, and back again. My pen photos still are lacking in contrast and saturation, and I'm working on that.
Good composition is harder yet. Presenting a pen in a dramatic and appealing fashion can be quite a challenge. Some of the photos on this site really catch the eye. It's the choice of props, backgrounds, orientation, reflection, depth (depth of field, color depth, contrast, and perspective), etc. that make some photos really stand out. Good photographers know how to get bling. I don't yet, but I'm trying.