Well, one of the biggest changes in the new MM (or at least the SRD--I haven't shelled out the cash for the books) is the new DR system. (IMO probably one of the worst changes in the revision).
The new DR system could be transferred to 3.0 (although why you'd want to is beyond me in most circumstances) however, you'd need to add rules/spells for aligning weapons. The simplest way to do so would probably be to say that the Magic Weapon and GMW spells grant the alignment qualities of either the cleric or the cleric's deity to weapons they're cast upon. (PC's choice at time of casting). That way, a Lawful good cleric of Pelor casting GMW on some arrows makes them both lawful and good aligned. The more complex way to do it would be to add the align weapon spell (although I'd recommend putting it in at first level rather than second like in 3.5--that way you'd avoid the silly 3.5 situation where you can buy oil of bless weapon for less than a scroll of align weapon and it's cheaper, doesn't need to be cast by a cleric, and auto-confirms crits in addition to aligning weapons to "good.")
Elementals also get DR 5 or 10/- instead of DR 10/+1 and 10/+2 as in 3.0 Without 3.5e power attack, this will be next to impossible for parties without wizards (and wizards with wands of magic missile at that) to deal with unless they're populated by high strength bull's strengthed greatsword wielding fighter/barbarians.
Otherwise, I suspect that 3.5e CRs will work reasonably well against 3e PCs.
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