I went to the Pitt Rivers Museum on Saturday, and noticed two things about their displays that I like.
They group objects together by function (e.g. musical instruments, writing and communication, clothing, sympathetic magic, religious iconography, etc) and include items from Europe among items from other cultures. This allows the museum audience to see how things have a similar function and morphology across all cultures (instead of marveling at the so-called "primitive" Other), and sets objects in a different context than if they were arranged by separate cultures, as they are in most other museums.
The labels are next to the exhibits, which means you don't have to cross-reference from a number next to the object to a list of numbers on a panel at the bottom of the case. (Sadly the Ashmolean has gone for the numbered labels system, which makes it very tiring to view objects there. The only exceptions are the galleries of paintings.)