Quantum dots, semiconductor nanocrystals, have unique optical properties, including narrow emission bandwidths, broad excitation spectra, and remarkable photostability, which have made them excellent candidates for biological imaging. Since their introduction into the biological milieu in 1998, they have been applied for in vitro and in vivo imaging, diagnostic testing, and multiplexing. As researchers have appreciated the benefits of quantum dots for imaging, emphasis has shifted to fabricating nanocomposites containing quantum dots, and among these magnetic quantum dots have attracted significant attention. Here, we describe our efforts to fabricate quantum dots and magnetic quantum dots. Highlighting our most recent efforts in this area, we will describe our development of micellar surface coatings, which permit multiple quantum dots to be incorporated into a nanocomposite with similar size to traditional commercially-available water soluble particles. These MultiDots display dramatically enhanced nanoparticle brightness and photostability, with a reduction in blinking behavior, and can emit fluorescence in two wavelengths. These particles thus have advantages in diagnostic testing and single particle tracking applications. Next, we will discuss the synthesis of specialty, switchable quantum dots, whose fluorescence can be optically controlled and their potential application to super-resolution imaging (e.g., STORM). Finally, our efforts to develop magnetic quantum dots will be described. We have identified three different synthetic routes to these materials, the most promising of which is micellar co-encapsulation yielding MagDots. Using MagDots, we will describe application of these particles to cell separation, molecular separation, and supramolecular assembly and manipulation of microtubule proteins.