Okay, so apparently there is no preferred method for this:
The following seems to be working:
if (!Page.ClientScript.IsClientScriptIncludeRegistered("MyControl.ascx.cs"))
{
Page.ClientScript.RegisterClientScriptInclude("MyControl.ascx.cs", ResolveClientUrl("~/scripts/myjs.js"));
HtmlHead head = (HtmlHead)Page.Header;
HtmlLink link = new HtmlLink();
link.Attributes.Add("href", "~/css/mycss.css");
link.Attributes.Add("type", "text/css");
link.Attributes.Add("rel", "stylesheet");
head.Controls.Add(link);
}