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This depends one your configuration. If you have a dual boot setup with any version of Win 9X that is OSR2 or later then you should use fat 32 as these OS cannot support NTFS. However if you have only an NT based Os (ie winNT or 2K ) then you should use this as it is far more efficent at storing files. NTFS also has built in compression and encryption, which is most useful on a laptop, as these often have smaller HDD and the encryption means that if somone steals it they are less likely to be able to get personal details off it.

In my case I use Fat 32 on my main machine as I have a dual boot with win me to run any programs that I can't get to run properly in win2K (there only is one, Black and white). On my older machine it is a straight win 2K box and it has NTFS with compression (the HDD is only 6GB).
 
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NTFS is more secure than FAT32, but because of this security, you cannot write to it properly from other OSes, such as BeOS, Linux, FreeBSD, etc.. If you plan on running multiple OSes, FAT32 is the better choice...
 
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