+1 ... I've got clear b+w protection filters on my lenses with no iq drawbacks - some lenses even require a filter for full sealing. I'd like to add that polarizers mostly don't work with wide-angle due to too different angles towards the sun. I thought grad filters are analog old-school, but after what briansquibb wrote maybe I should think again? How often do you use them (for static scenes I'd just do hdr or exposure fusion, that's when IS comes in handy, too)?
ND Grads are good in that they can reduce the DR of the scene, therefore allowing better details to be captured.
The traditional use is to have a scene with a bright sky and dark grass/trees etc. In summer the bright sky totally overpowers the ground, so you end up with blown out sky or near black ground , depending where you are metering.
By adding a grad with dark at the top and light at the bottom you reduce the light coming from the sky whilst not affecting the light from the ground - which means you can capture detail in the sky as well as the ground as the by reducing the sky light you are reducing the DR of the scene - by several stops. This means that in this case a 5DIII + ND Grad would be able to capture the same detail as a D800.
I like using ND grads for low light street scenes where the dark part reduces the light level of the street lamps
I also have used 2 together, blue and red for sunsets on the sea. I put the dark red on the sky and the dark blue on the sea - gives spectactular colouring.
I use Cokin/Lee filters