Great question! Just last month I transformed a closet into a playroom for my daughter and son. My goal was to create a shared space that made each child feel like an individual. I was able to stow the majority of their toys into bins placed on the Ikea Expedite bookcase. The bookcase is simple, the bins are the same, yet what is inside is what makes each child happy. Then I gave them each their own table, important for coloring and playing. Above the tables I took Ikea photo ledges and made them each their own small library. They each picked which books would be in their own library! Also, I hung Ikea dog tail hooks for them to each hang their own costumes. The hanging of costumes looks fun and festive, and affords us more space in the bins for stuff that doesn't "show well." Truly the space was unified keeping the basics neutral and allowing the gender of each to speak through their own book choices, costume choices and choices of toys inside the bins. Here's the post: http://hamptontoes.blogspot.com/2011/10/from-closet-to-playroom.html
What I did with the playroom is applicable to a bedroom that is shared by two opposite gender siblings. Take two of the same upholstered headboards, have their own monograms stitched into the textile, use the same duvet cover, yet allow each child to pick their own sheets. Or use two of the same striped duvets, yet allow each child to pick his/her own color. Create a library for each child with the photo ledges, the books each child picks will speak to him or her yet using the same ledges will pull the look together. At the end of each bed anchor the space with a table and a couple of small chairs for each child.
There are so many options, but I think the key is to create one space that is visually appealing and functional, yet allows each child to be an individual. Usually this can be easily pulled off by keeping the basics neutral and bringing the color in through the books and toys.