Multisite – Site Specific Modifications

I have a multisite that has 3 different themes (1 parent, 2 child) that server many different clients. Inevitably, these clients want small changes made that don’t necessarily warrant an entire separate child theme, but code must be added nonetheless. Think changes like nav color, a footer element removed, an extra call-to-action added; little changes like that which generally require PHP conditionals added to the templates.

Making these site specific changes, usually wrapped in a conditional that checks the blog ID, is difficult to manage and keep track of, and makes my templates messy. What I want to know is if there is a way to accommodate these small edits in an elegant fashion. Maybe an area where I can paste in some PHP, which will only affect that specific sub-site? A comprehensive options page that covers all customizations?

I’m not sure what approach will give me the most streamlined, manageable solution.

Thanks in advance for your suggestions!