For subwoofer applications, I only line the cabinet walls with damping materials, particularly a very high density egg-crate foam that is available only available to other companies commercially. Stuffing can not only raise the cutoff frequency, but it can restrict airflow and alter other resonances.
However, you can lightly stuff a vented box in some cases, such as smaller midrange applications. Here, you can be less concerned with the monumentous amount of airflow associated with some of todays bass drivers, while still cleaning up some midrange "muck". However, it is still advisable to leave an unblocked channel admist the stuffing from the back of the driver to the port tube.
(By the way, I own a pair of Mirage speakers which are indeed stuffed, but fairly lightly aside from the damping on the sidewalls. Also, the stuffing material seemed to be a "long haired" material, which is arguably better sonically. Long haired wool is rumored to be one of the best materials to stuff with, though its scarce availability and price don't allow too many people to test it.)