Windows cant recognize the ext3 system, so it wont show in windows at all.
NTFS system works for both, but isnt so good for linux instead, some minor problems will popup some time, like: cant write to that HD in linux, need a software to help you with that. Sometimes it gets corrupted when mounting it for the first time, also pain in the butt to fix.
The main question is:
Will you use only Linux or Linux + windows with that harddrive?
Only Linux, then ext3 is the right system.
Win + linux, then NTFS is the right system.
Dont use fat32, as it cant handle big files etc...only gives you more headache