Specto, it's entirely possible it's multiple addons interfering with each other.
As for an approach to determine it that isn't just enabling/disabling addons hoping to figure it out, there are a couple options:
Some mods list "known conflicting" mods on their descriptions, but that's not particularly common these days. But hey, if you're at work and can't actually log in for the next six hours, might as well browse the websites/descriptions/forums for every mod you installed and see if they list any problems!
There are mods that track cpu/memory usage, and display it. You could get one of those, and watch it and see which either uses the most, or which one spikes/increases a lot during the stuttering.
There's also simple logic, if you know much about how the wow interface works. For instance, I have found that bag mods are notorious for doing a whole lot of calculations on a pretty regular basis. If the stutter happens when you loot an item, but generally not if you're just jumping around in circles, it might be a bag mod. If it happens when you mouseover a mob, it might be a tooltip mod.
Obviously, these are just hints that might narrow in. It's always possible you installed a mod that some less-experienced coder wrote, who hooked the "ON_UPDATE" which runs at your FPS, and did tons of calculations on each one, but he never noticed 'cause he has a six thousand dollar desktop to play wow on, and neglected to think of those of us who are stuck playing it on a five hundred dollar laptop.
Another way to narrow in, often mods that have similar areas of focus conflict. If you have two tooltip mods, or two nameplate mods, even if it logically seems like they should work together, they probably both hook all the same things, and one might screw the other up.
Then, of course, there's the completely illogical ones. Carbonite's map has serious problems with Wintergrasp timers, and tooltip mods that are acceptably fast could have a huge impact on inventory-scanning mods (like bag mods), since a lot of mods scan hidden tooltips quite frequently, and if those tooltips are taking five times as much CPU to build due to tooltip mods, it might add up. Who knows.
Basically, without your list of mods, there's no way we can theorize anything specific. Even with it, we could only guess unless it's a well known issue. There's a couple tools, and some basic logic, but the only way to know for sure is to just power through.
-x