is it a question about the layout? or the system that you guys want to developed? as what ive experienced developing a custom web framework... it depends on how you want it or what features you want... i suggest make it modular... like what i did on my bayanihan cmf its modular... it can run as standalone site, it could be social network... and job posting classified directory or just a web application... just make modular... put a common door where components can pass... always use callback to avoid rewriting the core system...
coding a modular system is not easy... it takes carefull preparation, compared to a feature specific... but in a modular system it has room for additional features and improvement... with less recoding...