From my (somewhat limited) Linux experience, there are the following choices:
ext2, ext3, ReiserFS, XFS
I think there might be some others, but these are the most common. Ext3 is supposed to be reliable, ReiserFS is fast, and XFS is...something else. Anyway, each has its advantages and disadvantages from what I've read. Personally I chose ReiserFS since it's supposed to be fast and pretty reliable as of the later renditions.