Well if you are going to combine the operating systems I would recommend going with a fat16 or 32 partition for your filestorage (if you have no security concerns). If you make the filesystem NTFS you can mount it and read from it from linux, but you won't be able to write back to it. Make the Boot partition fat16 or 32 also.
What you choose for you windows OS depends on what you want to do. Lots of media access (scanners, digital cameras, etc) then I would choose XP. Also, if you have any legacy apps then I would choose XP also. It has a better compatiblity mode than 2000 Pro. You can also strip the visuals out of XP and improve performance.
If you don't have to have it I would also recommending disabling system restore and drive indexing. If something goes wrong its just an opportunity for me to clean install anyways. Then again, if you don't want all of these extra features then 2000 might be ok for you. Just remember XP will be supported for two years longer than 2000 will, including bug patches, etc.
Check this thread here at Anandtech for the consensus on NTFS partitions:
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