Plants: Having a bit of greenery instantly makes your cube less dull, and getting up to water your plants also gives your eyes a break from the computer screen. Pothos works well in my indirectly lit office, or you can try Sansevieria or a peace lily.
Pen holder: You most likely have a handful of writing utensils that need wrangling. At my day job I use a small pottery vessel in my favorite color and that was made by a former coworker. Find handmade and vintage options from Etsy, or seek out Marimekko's latte cups. The cheapest solution is to use a (cleaned) can and cover it with nice paper à la SusyJack.
Mousepad: You'll be using it all day, but its appearance is often overlooked. Check out an Etsy seller such as MirrorGirl or follow this easy tutorial to make your own with a $0.99 pad from Ikea. (On a similar note, make sure your setup is ergonomic by following these guidelines from the U.S. Department of Labor.)
Lamp: Overhead fluorescent lighting is pretty terrible. As an upgrade, find a task lamp that has some personality and a nicer glow (Image 1). Kristen recently rounded up ones that are under $50, and there are lots of other affordable options.
Calendar: Hanging art is a great way to personalize any space, but sometimes it's just not an option in an office. Instead, consider a desk or wall calendar that speaks to your aesthetic. In December Apartment Therapy rounded up calendars with mid-century modern style, travel themes, and great letterpress looks. From our 2010 Home Hacks, you can also try making your own perpetual calendar.
Do you have any decorative touches in your office?