You just have to weight paint manually after having automatic weights applied. Automatic weighting does a very good job, but usually it seems to get 95% of it. That last 5% (like the inside of a mouth or exents of the head or limbs) is what you have to get.

However it's not too hard, and you can even select bones to see the vertices that are weighted to them... I found a video that explains it. (I even remember seeing a better video, but can't seem to find it again. This one lays out the basics needed to do it though.)

https://www.youtube.com/watch?v=W_sfan8OchA

One last bit... If I recall, if some stray verts are a problem you may need to check the auto-normalize and/or multi-paint options. Also you can re-pose and go back to weight painting to get those pesky stray vertices assigned to the proper bone vertex group. (Not to mention re-posing before going back to painting makes it really obvious which verts aren't moving with the armature as they should.)

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Barbequed Pixels?

Your friendly neighborhood Wings3D nut.
Also feel free to browse my freebies at ShareCG.
There might be something worth downloading.