What system do you use to manage your home directories, and how have they worked for you for managing small files (e.g. dot configs) and large (gigabyte binaries of data) together?
I don't know that managing them *together* is all that useful. What I have been doing (and what I think is a more flexible way to manage stuff), is to divide the stuff in your home directory into independent 'projects' (e.g. financial documents, stuff for work, source code of my website, project X, project Y, my photo collection...) and manage each project separately in a way that lends itself well to the kind of file being stored. For a directory of small files that are frequently updated, Git is a great way to go. For synchronizing and backing up large collections of large files (like an MP3 or photo collection) you might try something like ContentCouch (disclaimer: I wrote this tool).