There are a bunch of ways that you can accomplish this in WPF. Shown below is one:
<Border Grid.Column="1" CornerRadius="6" BorderBrush="Gray" Background="LightGray" BorderThickness="1" Margin="5" HorizontalAlignment="Left" Name="border1" VerticalAlignment="Stretch" >
<!--Add a grid control to separate your stackpanel and button-->
<Grid>
<Grid.RowDefinitions>
<RowDefinition Height="*"/>
<RowDefinition Height="Auto"/>
</Grid.RowDefinitions>
<StackPanel Grid.Row="0">
<StackPanel Orientation="Horizontal">
<Label Content="Dimension" Name="label1" VerticalAlignment="Center" />
<ComboBox Text="3D" HorizontalAlignment="Right" Name="dimensioncb" VerticalAlignment="Center" IsReadOnly="True" IsEditable="True">
<ComboBoxItem>2D</ComboBoxItem>
<ComboBoxItem>3D</ComboBoxItem>
</ComboBox>
</StackPanel>
<Separator/>
<DockPanel>
<Label Content="Iteration" Name="label2" VerticalAlignment="Center" />
<ComboBox Text="3" HorizontalAlignment="Right" Name="iterationcb" VerticalAlignment="Center" IsReadOnly="True" IsEditable="True">
<ComboBoxItem>1</ComboBoxItem>
<ComboBoxItem>2</ComboBoxItem>
<ComboBoxItem>3</ComboBoxItem>
<ComboBoxItem>4</ComboBoxItem>
<ComboBoxItem>5</ComboBoxItem>
<ComboBoxItem>6</ComboBoxItem>
<ComboBoxItem>7</ComboBoxItem>
<ComboBoxItem>8</ComboBoxItem>
</ComboBox>
</DockPanel>
</StackPanel>
<Button Grid.Row="1" Content="OK" VerticalAlignment="Bottom"/>
</Grid>
</Border>
The above XAML, used to replace the right-hand Border
in your XAML will produce the following result, and will keep the button on the bottom when re-sizing the window.