Немного красивее для mongodb.version () 3.0
db.collection.aggregate([
{$match: {created_at:{$exists:1}}},
{$group: {
_id: {$add:[
{$dayOfYear: "$created_at" },
{$multiply: [{$year: "$created_at"}, 1000]}
]},
count: {$sum: 1 }
}},
{$sort:{_id:-1}}
])