Donncha’s “It’s impossible to say” answer is the only one anyone knowledgeable about the issues could reasonably provide. Not only is that an incredibly long list of plugins no one is likely to have carefully tested in combination, but most of those plugins have a multitude option settings that can affect mutual compatibilities. Beyond that, users run WordPress with many types of hardware, under a variety of different computer operating systems, using a variety of different web servers configured differently, with different versions of PHP configured differently, with different SQL servers configured differently, and with many other variations.
Anyone who combines individually complex systems to form larger, much more complex systems, is running an new experiment unless they can find someone who as tried the exact same combination, including all the optional settings.
However, one thing that can be stated relative to this is that the chance that a relatively simple system can be added to an already complex one without conflicts is better than the chance that a relatively complex system can be added without conflicts. WP Super Cache is relatively simple compared to W3 Total Cache and therefore more likely to work.
Another thing I can say from personal experience is that not only is WP Super Cache simpler to configure, but page loading times have been shorter and CPU workloads have been lower using it in combination with Autoptimize compared to using W3 Total Cache during exhaustive tests at multiple sites. It is easy to understand that finding technically. However, it could be different for some users depending especially on what their primary speed bottlenecks happen to be.
The only way to determine comparitive performance advanges and plugin conficts at other sites is to take Donncha’s advice to “Just try one and fix the problems you find” and then to measure preformance result differences. If that is too much trouble, you will never know with certainty which would be best.
