The following recommendation was put together Feb 2003 by the members of the Joint Engineering Team (JET). The JET represents a collaboration of leading United States federal and academic wide area networks, including: Abilene (Internet2), DREN (DOD), ESnet (DOE), NREN (NASA).

JET-wide Recommendation on IP MTU

Engineers throughout all components of the extended JET infrastructure, including its campus LANs, its gigaPoPs, its backbone(s), and exchange points, are encouraged to support, wherever practical, an IP MTU of 9000 bytes.

The rationale for this recommendation includes the following points:

Applications, including but not limited to bulk TCP, benefit from being able to send 8K (i.e., 8 times 1024) bytes of payload plus various headers. An IP MTU of 9000 would satisfy this application need.
A growing number of routers, switches, and host NICs support IP packets of at least 9000.
Very few routers, switches, and host NICs support IP packets of more than 9500. Thus, there is comparatively little motivation for a value much more than 9000.
There is anecdotal evidence that Path MTU discovery would be more reliable if a given agreed-on value were commonly used. This relates to bugs in some Path MTU discovery implementations.
9000 is an easy number to remember.

It should be stressed that this is an interim recommendation. Engineers are also encouraged to work over the longer term to explore the benefits and practicalities of much larger MTUs, up to 64 KBytes permitted for an IPv4 datagram and beyond 64 KBytes for IPv6.