Basically the dropdown, lists all the document libraries in a site that you have access to.
You will have to change the "RteUploadDialog.aspx" in the Layouts folder in the 14 hive to accomplish this. Search for the Dropdown "TargetList" and add a line similar to the code below to get the document library you wish to get selected. Here I have made "Documents" Library as my default selected value.
<asp:DropDownList id="TargetList" onchange="CheckUniquePermissions(this.options[this.selectedIndex].value);" Width="320px" runat="server" DataTextField="Documents">
<asp:ListItem Selected ="True" Text="Documents" Value="2fd2a13d-3c11-4bf0-8638-6ddfd45c35cb"></asp:ListItem>
The ID of the library can be retrieved by getting the view source of the popup page. Everything should work fine, but I would not recommend editing the core files inside the layouts folder which could breach your warranty with Microsoft.