RRS, I'd say HL2 has clearly won the match against D3. Simply because of the sheer variety of scenarios and situations. Although in defense of Doom3, I'd have to say I rather wanted it to be a remake of the old Doom games - so basically that's what I got in a technically brilliant fashion. My gripes with D3 are more along the likes of "does not look as good as HL2 on old computers".
Half-Life 2 looks a lot better on older computers than Doom3 and HL2DM > D3DM, imho.