The NIST SP 800-73 standards for PIV are
available free of charge on the NIST web site. You probably want to be looking at the SP 800-73-3 standards.
The Yubico Neo PIV applet doesn't strictly follow the standard in some respects. The PIV standard says that only the 9E slot should be available via a contactless interface - 9E is primarily used for physical access control applications, hence the value of contactless. The Neo makes all slots available via contactless.
From what I remember of the PIV standards, 9A is used for a logon certificate, 9C for digital signing such as signing S/MIME e-mail, 9D for decryption of encrypted S/MIME e-mail, and 9E for physical access control.
In practice, you can use 9A, 9C and 9D freely according to your applications. I have my StartSSL client certificate in 9A and my StartSSL code signing certificate in 9C (where the requirement to enter the PIN every time is an advantage). I have no real use for 9E as I don't have any access control infrastructure, whilst 9D is spare in case in need a client certificate from another CA.