Herolab does if you download the community patch, it's not 100% accurate, but it's good enough
Classic. I use it often.
The program? Getting used to the interface is probably the only real problem I have. I picked up the iPad app while it was still available a while back and use it almost exclusively, as the interface is better for me. The only downside is that I can't fiddle with the configuration files to create my own classes or paks.
As for using the gestalt option from the community pack, its not difficult at all. You just make sure the option is turned on, and you add a level of 'gestalt' followed by a level of each of the classes you are gestalting at that level, and then use the tab specifically for Gestalt options to assign those classes. The program handles pretty much everything properly aside from the CR ranking of the character, since it is artifically inflated due to having 3 classes per every 1 it is expecting.
There are some inherent issues it has with classes like Evangelist or Mortal Usher which boost other classes, specifically in instances when you boost Evangelist WITH Mortal Usher to further boost an original class. Something doesn't connect in those instances.
I don't think that Hero Lab classic has the gestalt ability any more. It was a "Community Package" add-on that was not supported by the studio that publishes Hero Lab. It relied on a separate community infrastructure that is no longer being supported. The user who maintained both (for free!) no longer does so.
At least, that's what I found when I went to create a gestalt in Hero Lab back in July. I haven't seen anything that indicates otherwise after a brief check.
*********
I played around with PathCompanion recently, which has gestalt support if you turn that option on in the settings. I don't recall having any issues with it, but I ended up just creating the gestalt PC mostly manually. I can't remember exactly why.