Most providers I have used offer a free app through the App Store that will give you details on your 3G usage. In my experience, they only work when you use them while you are ON the 3G network, not when you are on Wi-Fi.
The apps will not tell you WHAT app, if any, is using 3G, they will just give you a breakdown of how much you're using.
In the meantime, you can try making sure you're not running a music app in the background on 3G (other than the iPod which of course doesn't use 3G) or something like that, turn off push notifications on apps that would tend to use a lot of data, make sure your Skype or chat programs are actually logging you out after a certain amount of time or "on close," etc.
