The answer, as always, is “it depends”.

NFS pros:
Supported by lots of vendors, therefore more choices
Cross-platform between OS X and Linux/Solaris/etc
Supports fast user switching
NFS cons:
Security model may not fit your environment
Some filesystem attributes not directly supported

AFP pros:
Native Apple solution, so best Apple support
Filesystem attributes closest match for HFS+
Easy to set up and run from Apple hardware
Best support/fit for Portable Home Directories
AFP cons:
More limited support for AFP on non-Apple hardware/OS servers
Not cross-platform
Doesn’t support fast user switching

You’ll have to decide which bits are most important for your environment. NFS homes are a good fit for us, but might be a disaster in a K-12 environment…

-Greg