if you havn't updated recount/skada since 4.1 came out, old versions of them are known to cause horrible performance, for one place to check. I personally recommend using the curse downloader, it makes it really easy to just flip open my system tray and see if I have any out of date addons (as far as addons that are hosted via curse are concerned, but most are at least mirrored there, so its fine) , and it takes just a click per addon to update, or just one click to update everything if you pay curse some whatever per month which I do not.

Curse Downloader doesn't work in Linux, I use WowInterface Minion it's cross platform and it's very good. It also has a update all button you don't need to pay for.

You can use addons to find misbehaving addons. I personally use Chocolate Bar http://wow.curse.com/downloads/wow-addons/details/chocolatebar.aspx plus Broker_CPU Memory http://wow.curse.com/downloads/wow-addons/details/brokercpu.aspx
It tracks memory usage of all your addons and, if you turn on CPU Profiling, it will tell you how much of your CPU each one is eating up (you do that just for testing as CPU profiling being on tends to eat a lot of resources itself). Any misbehaving addons will be at the top of the list.

It won't find the ones that are slowing things down by spamming errors (turning on Show LUA Errors in the interface menu will show you those) or certain other issues, but it will find most offenders.