What level of simulation are you looking for, and how much are you willing to spend?
For example, there is this:http://www.labcenter.com/products/vsm/avr.cfm
It costs about $500.00 for a license. It will likely do everything you need, though. Probably has a fairly steep learning curve (it is a SPICE simulator).
I don't know anything about its quality or accuracy; I don't own it, and I've never used it.
Software like LTSpice can help you when it comes to analog designs (and it's free), but you won't get any microcontroller simulation with it.
Regardless of what you use, no simulation will be 100 percent accurate, nor will a simulation that runs perfectly necessarily work the same with real-world parts...