I've tried using CR with Pathfinder, 4e and 5e, and so far, I wind up ignoring it or trying to reverse-engineer it to make sense to me.
My usual stumbling point is that the system assumes a party of X characters and one monster as it's base value. And I rarely use just one monster in an encounter. So I'm almost always having to apply some kind of modifier.
Anybody like it? Using it sucessfully?
I pretty much rewrote my entire system around fixing the CR system and its somewhat in line with the "CR-There Is a Better Way Part 2" article that Steven Mitchell linked to upthread.
The real honest to God key to a functional CR system from my experience (and why its never worked all that great in D&D) is that for it to be able to reliably measure anything you need the system to have linear instead of quadratic scaling.
In D&D, your improvement in combat is generally quadratic. Not only are you becoming more accurate, you're also dealing more damage per round. You're not only getting more hit points, you're also getting harder to hit.
So instead of five 1st level threats being of similar danger to you at 5th level as one was when you were 1st level. Its likely you'd need ten or even twenty (and maybe more) to present a credible threat to the PC. The result is that your challenge rating has to be quadratic if its going to measure anything accurately... Ex. a level 1 is CR1, a level 5 is CR10, a level 10 is CR40, etc.
But even that has its limits because, in 3e/4E, the scaling was so great that often a 10th level PC was virtually immune to any number of 1st level threats. 4E even directly referenced this with statements about how a solo monster at level 1 would have to be restated as an elite if facing the PCs at level 10, as a standard monster at level 20 and as a minion if the PCs encountered it at level 30. In one epic tier adventure they even statted up a legion of thousands of ghouls (heroic tier threats) as DIFFICULT TERRAIN for the PCs during a fight with an Exarch of Orcus.
My solution to creating a fully scalable and easily usable CR system (also a system that allowed mass battles without needing special conversion rules... the original purpose of the change) was to remove one of the axes of growth so that level progression was linear. Specifically, to-hit and defenses are almost static; about +10% over the entire range of the game; while damage and hit points scale linearly for both PCs and monsters.
The result is that you can more-or-less just use a monster's hit points to determine its relative threat to the PCs*. If a PC has 25 hp, then a group of monsters with a total of 25 hp will be a normal challenge for them. If an adventuring party has 220 hp, then monsters with about 220 hp will be a normal challenge, 330 hp will be a dangerous fight and one with 440 hp will almost certainly result in a TPK if the PCs don't beat a hasty retreat.
This also makes it easy to account for henchmen and hirelings in encounter balance too. Just add their hit points to the PCs side to determine what's going to be an easy, typical, hard or lethal fight for them.
* Its slightly more complicated than that since monsters can trade hit points for better defenses and visa versa, and can trade accuracy for damage and visa versa (that way there's more variety than just level between monsters); but the default "Challenge Point" value is just the pre-adjusted hit point total of the monster with everything else about the monster scaling in ratio with that.