If you think that a wizard with his spellbook and component pouch is able to take the same challenges as a wizard with a +3 cloak of resistance, +4 headband of Intellect, Clvl 7 wand of magic missiles, three pearls of power and a selection of utility scrolls stashed in his Handy Haversack you're greatly mistaken.
The same is true for a cleric. The cleric in scavenged studded leather with a quarterstaff and an improvised holy symbol is not able to take the same challenges as a cleric with +2 fullplate, a +2 cloak of resistance, +1 Holy longsword, +1 buckler, +2 periapt of wisdom, pearl of power and a wand of cure light wounds.
And an 8th level fighter in his underwear with a normal longsword is still quite capable of great-cleaving (or whirlwinding) his way through hordes of low level foes.
All characters suffer from not having equipment and none are completely shut down. (Although some are hurt more badly than others--the monk is probably the least equipment dependent character class and the fighter the most equipment dependent with others falling somewhere in between).
So, I'd recommend doing two things. First, tone down your base assumptions about what PCs can handle by one to three CRs. And second, evaluate them individually for challenge. Abilities like rend which depend upon hitting multiple times (much more likely when the PCs are poorly equipped), mass incapacitating spell like abilities (frex, the Mummy's despair ability; PCs are much less likely to save without their resistance items), and DR (DR /adamantine is much more difficult to overcome without adamantine weapons (or magic weapons whose plusses can be converted into damage to overcome the DR through power attack)).
Halivar said:
If ti's high level, the casters are probably less affected by the loss of equipment. I'd go ahead and peg their CR's the same as before. But the fighters... yeesh... can you even give them a CR? I suppose they can grapple or something.
