D&d 3.5 question on challenge rating for altered monster
Really depends on the monster. If it has spellcasting and usually avoids melee, keeping the same abilities and being harder to hit (and having an easier time hiding) is wholly beneficial. If it's meant to be involved in melee, it'll be a lot less effective...
Taking humanoids as an example, you have Medium humanoids ranging from CR 1/2 (Orc) to 3 (Bugbear), Large going from 4 (Ogre) to 10 (Fire Giant), and Huge going from 11 (Cloud Giant) to 13 (Storm Giant). So the reduction in size (and special powers) could be in the 12 CR range (Storm Giant to Orc). If you look at the transition to Ogre from Bugbear, it's a +1 CR, so going from Huge to Medium would be more like -2 CR.
A range of monsters that increase in size as they gain hit dice seem to change size when their CR goes up by ~2 or so, suggesting that a size increase (with extra hit dice for even bigger numbers) is worth around 2-3 CR. This work with the Orc -> Ogre transition. So going down in size without losing hit dice would probably reduce CR by 1-2 per step.
Again, it really depends on what you're looking at and how affected it is by the size change.