They passed the joint matrices as uniforms and vertex weights and indices as attributes using VBO's
I was wondering, is this how it is commonly done?
Yes, this is the standard. Since each vertex is affected by a different set of bones, you will need random access to the bone matrix palette in the vertex shader. The nice thing with this approach is that the VBO data stays always constant, and only the uniforms change.
The other sometimes seen option is to store the bone matrices in textures, and sample the textures from the vertex shader to read the bone matrices. This is done just to avoid the upper limit on the number of constants one can have, since texture memory can hold much more data. This method requires Vertex Texture Fetch support.
If you need more than four bone influences per vertex, you can use multiple vertex attributes for that, but that naturally increases processing costs. Using four influences is a kind of middle ground, and fits nicely to 4D vectors.