I don't know about "best" but OrCAD Capture is very widely used. Most of our clients request that we work with Capture (perhaps be cause it's not outrageously priced). Reference designs from other companies (like Atmel) are supplied in OrCAD.
There are some rough edges, but it's what we (still) use. BTW, 9.2.3 seemed most stable. And it is still possible to download that old dog (if you have a current license!)