[tsigel]

var obj = {
    "database.host": "127.0.0.1",
    "database.user": "test",
    "database.password": "qwerty",
    "rest.photo.host": "127.0.0.2",
    "rest.users.host": "127.0.0.3",
    "rest.users.password": "p@ssw0rd",
    "baseUrl": "test.com",
    "limit": 10
};

var result = {};

Object.keys(obj).forEach(function (name) {

    var path = result, names = name.split("."), len = names.length;
    names.forEach(function (subName, index) {
        if (!path[subName]) {
            if (index == len - 1) {
                path[subName] = obj[name];
            } else {
                path[subName] = {};
            }
        }
        path = path[subName];
    });

});

alert(JSON.stringify(result , "", 4));