beveled buttons are the staple of any gui-based application...you click them and they do things. people are comfortable with them. therefore, you should use them on your web site as a navigation tool...preferably in combination with a sidebar of some sort. here are a few additional tips:
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the bigger the bevel, the more important the button is.
grey is a good color for buttons.
oval or buttons with rounded corners are cool and good for a change of pace, but might confuse users because they are not rectangular.
the javascript rollover technique works quite well with beveled buttons...you can change the color of the button when the user rolls over it with their mouse. that way, the user knows that their mouse is actually on the button.