type    count
level1/level2/level3/Foo    24
level1/level2/level3/Bar    2
level1/level2/Baz   28
level1/level2/Quz   3
...

d3.tsv("data.tsv", function(error, data) {
  data.forEach(function(d) {
    d.count = +d.count;
  });

  // define key functions for a depth up to 4
  var nestedData = d3.nest()
     .key(function(d) { return level(d.type, 2); })
     .key(function(d) { return level(d.type, 3); })
     .key(function(d) { return level(d.type, 4); })
     .entries(data);

  // create the key for a specified level
  function level(type, l) {
     var parts = type.split("/");
     var result = "";
     for (i = 0; i < l && i < parts.length; i++) {
        result += parts[i];
        if (i < l-1 && i < parts.length-1) {
            result += "/";
        }
     }
     return result;
  }
  ...

function rollupFn(group) {
    var leaves = [],
        groups = [];

    // Split the items into leaves and groups
    group.forEach(function(item) {
        // First eliminate level already accounted for by d3.nest key
        item.type = item.type.substr(item.type.indexOf('/')+1);

        if (item.type.indexOf('/') > -1) {
            groups.push(item);
        } else {
            leaves.push(item);
        }
    });

    // Convert the "group" items into a d3.nest object
    groups = d3.nest().key(function(d) {
            return d.type.split('/')[0];
        })
        .rollup(rollupFn)
        .entries(groups);

    var results = [];
    if (groups.length > 0) { results.push(groups); }
    if (leaves.length > 0) { results.push(leaves); }
    return results;
};

var nestedData = d3.nest()
    .key(function(d) { return "level1" })  // optional: first group contains everything
    .rollup(rollupFn)
    .entries(data);