On the whole I find the CR/EL system to be quite good, but it of course has a few oddities. TiQuinn says it well. Just because a monster has a given CR, doesn't mean that all parties will find it equally challenging. Nor should they, IMO.
I do feel that once you get away from CR and start computing EL or otherwise playing with the system, that some ammount of DM subjective fudging is in order. For instance, it is not gauranteed that doubling the HD of any two given monsters will increase the challenge by the same ammount. Some monsters with double hit dice are only slightly more challenging than before. Others when doubled elimenate many of the weaknesses that made them low CR monsters and become quite fearsome. Similarly, doubling the number of creatures does not necessarily increase the EL by two against parties of any given level. This is adressed in a limited fashion in the DMG when they discuss doubling the number of Orcs, and whether or not multiple Orcs remain challenging at higher levels. In general, they rightly assert that they do not, but they don't go on to discuss why or in what circumstances doubling the number of monsters will produce scalable challenges.
I find, in general, if the CR of the monster is below the level of the party, doubling the number of monsters increases EL by one - not by two. Doubling the number of monsters with a CR equal or higher that the level of the party does increase the EL by two. This is because monsters of much lower CR than the parties level lack the ability to regularly penetrate the parties defences, and can be wiped out quickly (if needed) with area of effect spells. You would expect this because the DMG suggests that a party should be able to handle a large number of encounters with EL's two or more lower than the parties level without significantly reducing the parties resources. However, thier are exceptions to this. Some monsters of relatively low CR have abilities that remain dangerous to higher level characters, and which stack well with other like monsters. For instance, incorporeal monsters with touch attacks (like shadows or wraiths) will get by the defences of even high level parties fairly regularly. In fact, any touch attack is likely to remain dangerous - lantern archons and arrowhawks for instance. Relatively weak monsters with breath weapons and spells (like mephits) can with numbers do irratating ammounts of damage to even relatively high level parties. Low CR monsters with exceptionally high strengths (like dire monsters, the bigger vermin, or ogres) can in sufficient numbers continue to be a challenge to parties well into the mid levels because they can overcome AC so easily. Any creature that provokes a nasty save that stacks with other such creatures (that is successfully saving against one does not protect against the others) like vargoilles, rust monsters, or even monstrous spiders will continue to be a sourse of fear to higher level characters if you continue to increase the numbers.
