I just checked NASA's Discovery Missions and New Millennium Program websites. I didn't see any references to things like ion propulsion on the Discovery Missions site. Given the tight budget constraints on these missions, that isn't too hard to understand.

The Space Technology 7 (ST7) test vehicle is supposed to use a solar sail. That's pretty cool.

I don't see any new missions using ion propulsion but that doesn't mean none exist. I just might not be looking in the right places.

Ion propulsion is good for long missions that are relatively close to the Sun (assuming solar power). Ion propulsion like that used on DS-1 requires over a kilowatt of electrical power. That's quite a bit of electricity, especially if you're talking about using solar cells and are heading for the outer planets. That's also quite a bit of electricity if you're talking about using RTG power. Most RTGs put out a lot less electricity than that.

I was kind of surprised to see that the MESSENGER (Mercury Surface Space ENvironment GEochemistry and Ranging mission won't use ion propulsion, but I guess they just couldn't fit that into the budget constraints. Pity.