I am using the page icon value to store a large logo for the page... I have a custom control that uses this and works quite well. The problem is I can't work out how to prevent them showing up in the menu. I have set a CSS parameter in my default.css like this:

.menuIcon 
{
    display: none;
}

but this only seems to work for the submenus... not the root one.

Can anyone help me on how to prevent all icons from displaying in the main menu?

Take a look through your portal.css file, I use it as a blank slate for my skin.css files. In there, you will see a defined style:

.MainMenu_MenuIcon {
}

Simply add the line:    display:none

.MainMenu_MenuIcon {
        display:none;
}

what icons are showing.. do you mean the triangular arrows?

Rob