In the "admin cp > forums > edit"   menu, the one where you can choose whether each forum is a Discussion, Category, Questions, or External Link,  
you might consider adding 3 toggle buttons:  Show side panel, show top panel and show bottom panel. 

I mean it wouldn't allow for Totally custom widget layouts per sub-forum, but it would allow a single sub-forum widget layout, distinct from the front page, that can be toggled in its different aspects to create a relatively similar effect, with substantial versatility.

I know the whole "custom widget per sub forum" is a popular request, but it just seems like this might be an easier way to execute it (or something similar enough) on your end, without having to store a custom widget layout for each sub forum.

I've done something  similar in 

and we're evaluating methods for header and footer blocks too