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Setting font size in pixels is the best way to ensure that the type appears at the size you intended (because percentages and ems are more likely to vary if a user has changed the default size of text in their browser).
Pixels are relative to the resolution of the screen, so the same type size will look larger when a screen has a resolution of 800×600 than it would when it is 1280×800.
You can also use pt for point sizes instead of px for pixels, but you should only do this when creating style sheets for printer-friendly versions of pages.
The default size of text in a web browser is 16 pixels. Using percentages of this amount, you can create a scale where the default text size is 12 pixels, and headings are sized in relation to this.