I have never ran across a stackup program that I was happy with. Honestly, I find that mathcad or Excel are the best at what I need to do. You just have to make sure you set everything up correctly.
We looked at a product called SigmundEdge 18 mths or so ago. It was the version of their software that works with Solid Edge, I believe they have other options for other CAD packages. They also had a more complex version that takes statistics & probablities into account. It had some interesting capabilities, I would have like to trial it, but I'm not convinced it was a silver bullet.
The two I have run across are both UG embedded. Tolmate and VSA. Both now owned by UGS or I guess now since Seimens purchased it owned by Seimens. In my humble opinion I believe Tolmate does a better job of analysis.
Scott
There are three main Tolerance Analysis packages that are worth your time. Vis-VSA, CeTOL, and 3DCS.
I have used both Vis-VSA and CeTOL for many years.
Sigmetix, the company behind CeTOL, has me teaching their Basic CeTOL classes. I been doing 3D tolerance analysis for 17 years, with 8 years at VSA.