.eps is usually a failsafe filetype, but an illlustrator 9 file usually compensates for most shops with 'outdated' digtal capability.
Different shops require different things, but I usually like to eliminate error as much as possible, so I usually like to create separate eps files for each color; as black filled areas, used to create the screens. They print these files onto transparencies to create the screens, so a no-brainer file per color (do NOT forget to include registration marks, however, or at the very least - some sort of registration to allow them to align the prints)

Also, definately account for slight mis-registration when printing, and create trapping where necessary. (For those not in the know - basically when colors 'appear' to overlap, allow for a 1/8" overlap of the underlying color, so that when the color on top of it may deviate slightly, the trapping allows what may result in a gap be, well, not a gap.

Of course, many shops will take a complete ai/eps file to create the screens in-house, which is fine - but I do the work beforehabd to prevent misinterpretations by the technicians.

Talk to the pre-press department of the printer you are using and find out what they need. I've worked with two different screen printers in the past and they both had different methods for processing art. Don't try to seperate the colors yourself! In the end you'll just be making more work for the pre-press department (which will then be added to you bill). The are the ones that will know what their print presses can do and not do and how the art should be best converted and seperated.

Convert fonts to outlines when sending over your files. One of the biggest headaches in Pre-press is font problems. Converting fonts to outline helps avoid this. (Though it also means that any changes to text must be done on your end and you'll have to send another file.)

Keep in mind the material it is being printed on. In screen printing you have only so many print stations to work with. If you are designing a 4 color process image going on to a black shirt, then you'll need an extra station for the base white color as well as Cyan, Magenta, Yellow and Black. I've seen a couple of designs come through where the designer made a design that needed more color stations than the printer actually had.