Cells can be stained in any container for which you have an appropriate centrifuge. You can stain in the test tubes that will eventually fit on your cytometer, although the large bottom diameter of these tubes will make it difficult to get consistent results with a small volume of staining solution. Eppendorf tubes are classical favorites because of their conical shape. Staining can take place in a small volume in an Eppendorf tube and then the suspension can be diluted to a full 1 ml for each washing step.
If you are staining more than a few samples and have a centrifuge with plate adaptors, consider using 96-well, round-bottomed microtiter plates. While the dilution factor in the washing step is not as effective in these plates (because the maximum volume is 200 ml in each well), the benefits that derive from not having to organize, label, and manipulate dozens of test tubes makes plate-staining highly attractive. Photocopy a template to use for identifying wells; plan the layout of samples in the plate with some thought in order to make addition of reagents easy. It usually works to add the antibody or antibodies to wells in advance while cells are being prepared, keep the plates covered in the dark at 4°C until the cells are ready, and then use a multi-channel or repeating pipette to add aliquots of the cell suspension to the rows of wells. Care needs to be taken not to drag antibody from one well to the next in this procedure. Although it takes a bit of practice to become confident about staining and centrifugation in plates, most people become converts very quickly.