I want to create and add some animated graphics to the features based on a query in ArcGIS Explorer, like some moving waves at the queried features.
Is it possible?
You can create an animated theme (layer) in ArcExplorer - KML/KMZ is best supported to do this
You need to create a timeline to have the layer animated.
As for graphic create a layered gif or png and add into ArcExplorer as a point feature.
For ArcGIS (9.2 onwards) there is the animation toolbar http://webhelp.esri.com/arcgisdesktop/9.2/tutorials/animationinarcmap_tutorial_index.htm