Using the IK Tab
These articles give information on using the IK tab for your models. You can utilize the IK functions to control things pertaining to $collisionjoints and $jigglebones (among other things). You can access these tools by clicking the hierarchy tab in the command panel and then clicking the IK button.
$jigglebones are bones that can automatically generate secondary motion without being animated. Making a $jigglebone in WWMT requires you to use the hierarchy tab in the command panel, which may be a new area for less experienced modelers.
Making a ragdoll requires you to use the hierarchy tab in the command panel, which may be a new area for less experienced modelers. Watch the video here to get a basic overview of how to make a ragdoll for Source.