Once you have a popup content defined, you can do anything with this content depending on the controls. For instance, if you are using an image as content, you can do anything with the popup that you can do with the image.
The following code shows how to animate a popup window.
<StackPanel>
<CheckBox Name="PCheckBox" Margin="10,10,0,0"
Content="Popup Window"/>
<Button HorizontalAlignment="Left" Width="129" Margin="10,10,0,0">
<Button.Triggers>
<EventTrigger RoutedEvent="Button.Click">
<BeginStoryboard>
<Storyboard>
<DoubleAnimation
Storyboard.TargetName="theTransform"
Storyboard.TargetProperty="(RotateTransform.Angle)"
From="0" To="360" Duration="0:0:5" AutoReverse="True"/>
</Storyboard>
</BeginStoryboard>
</EventTrigger>
</Button.Triggers>
Start Animation
</Button>
<Popup IsOpen="{Binding ElementName=PCheckBox,Path=IsChecked}"
PlacementTarget="{Binding ElementName=PCheckBox}"
AllowsTransparency="True"
PopupAnimation="Slide"
HorizontalOffset="150"
VerticalOffset="100">
<Canvas Width="100" Height="100" Background="Green" Margin="150">
<Canvas.RenderTransform>
<RotateTransform x:Name="theTransform" />
</Canvas.RenderTransform>
<TextBlock TextWrapping="Wrap" Foreground="LightGray">
Rotating Popup
</TextBlock>
</Canvas>
</Popup>
</StackPanel>