There's an ongoing debate on this issue, which you should find many hits on if you run a search on this site.
Throwing my 2¢ in, my understanding is that both NTFS and FAT32 are quite equal in terms of speed. FAT32 has a slight advantage on smaller partitions in some benchmarks, while NTFS pulls ahead on larger partitions. The difference is so minute, that I wouldn't base your decision on speed alone.
If you don't plan on having a multi-boot system with a Win9x/ME system, I would just go with NTFS. You'll get the added bonus of additional security if you plan on using it, also advanced file allocation that NTFS provides over FAT32.
~cdogg
"The secret to creativity is knowing how to hide your sources."
- A. Einstein