we can register client script in serverside also....if u 
want to  make it in serverside use this code...

ClientScript.RegisterStartupScript(Me.GetType
(), "script", "<script language=""javascript"">function1()
</script>")

(or)

Me.Page.RegisterClientScriptBlock("close", "<script 
language=javascript>javascriptcode......</script>")

I think there is no difference b/n those two....depending 
upon the situatio we can use any of these....

ClientScript.RegisterStartupScript(Me.GetType
(), "script", "<script language=""javascript"">function1(){}
</script>")

and 

ClientScript.RegisterClientScriptBlock(Me.GetType
(),"script","<script language='javascript'>function1(){}
</script>

above two methods use to add client side event to server 
side.

Difference between above two is that 

ClientScript.RegisterStartupScript will insert script 
before closing </form> tag.

and 

ClientScript.RegisterClientScriptBlock will insert script 
after form start tag <form runat=server > of the page.

string popupScript = "<script language='javascript'>" +
"window.open'PopUp.aspx', 'CustomPopUp', " +"'width=200, 
height=200, menubar=yes, resizable=no')" +"</script>";

 Page.RegisterStartupScript("PopupScript", popupScript);

                       OR

Page.RegisterStartupScript(me.gettype(),"somename","<script 
language=javascript>somefunction()</script");