Unless you need NTFS, use ext3. Unless you need FAT32, use NTFS. Mint handles NTFS just fine, but ext3 is faster, more robust, and more reliable.
You might want to look at these threads below to get a better picture of what your choices are and what you might want to do.viewtopic.php?f=90&t=10696&st=0&sk=t&sd=aviewtopic.php?f=18&t=11125
There is probably more stuff floating around just can't remember where right now. Post back if you have questions.