Large difference in index size when indexes are built incrementally ( as new documents come in ) - versus built at once ( ensureIndex, reIndex, repairDatabase ).

_before_reindex.js

/*
  SERVER: MongoDB 2.4.3
  NS: test.session
*/

/* AFTER INSERTING 20k DOCUMENTS */
db.session.stats(1024)
{
  "ns": "test.session",
  "count": 20130,
  "size": 17299,
  "avgObjSize": 0.8593641331346249,
  "storageSize": 37596,
  "numExtents": 7,
  "nindexes": 3,
  "lastExtentSize": 18664,
  "paddingFactor": 1,
  "systemFlags": 0,
  "userFlags": 0,
  "totalIndexSize": 13373,
  "indexSizes": {
    "_id_": 646,
    "sid_1_d_1": 1820,
    "dim_1": 10906
  },
  "ok": 1
}
db.session["$dim_1"].stats(1024)
{
  "ns": "test.session.$dim_1",
  "count": 1366,
  "size": 10906,
  "avgObjSize": 7.98389458272328,
  "storageSize": 12276,
  "numExtents": 5,
  "nindexes": 0,
  "lastExtentSize": 9216,
  "paddingFactor": 1,
  "systemFlags": 0,
  "userFlags": 0,
  "totalIndexSize": 0,
  "indexSizes": {
    
  },
  "ok": 1
}

after_reindex.js

/*
  SERVER: MongoDB 2.2.0
  NS: tracking.session
*/

/* RUN REINDEX */
db.session.reIndex()
{
  "nIndexesWas": 3,
  "msg": "indexes dropped for collection",
  "nIndexes": 3,
  "indexes": [
    {
      "key": {
        "_id": 1
      },
      "ns": "test.session",
      "name": "_id_"
    },
    {
      "key": {
        "sid": 1,
        "d": 1
      },
      "ns": "test.session",
      "name": "sid_1_d_1"
    },
    {
      "key": {
        "dim": 1
      },
      "ns": "test.session",
      "name": "dim_1"
    }
  ],
  "ok": 1
}

/* AFTER REINDEX - NO DOCUMENTS HAVE BEEN REMOVED */
db.session.stats(1024)
{
  "ns": "test.session",
  "count": 20130,
  "size": 17299,
  "avgObjSize": 0.8593641331346249,
  "storageSize": 37596,
  "numExtents": 7,
  "nindexes": 3,
  "lastExtentSize": 18664,
  "paddingFactor": 1,
  "systemFlags": 0,
  "userFlags": 0,
  "totalIndexSize": 8415,
  "indexSizes": {
    "_id_": 582,
    "sid_1_d_1": 1229,
    "dim_1": 6603
  },
  "ok": 1
}
db.session["$dim_1"].stats(1024)
{
  "ns": "test.session.$dim_1",
  "count": 827,
  "size": 6603,
  "avgObjSize": 7.984280532043531,
  "storageSize": 12276,
  "numExtents": 5,
  "nindexes": 0,
  "lastExtentSize": 9216,
  "paddingFactor": 1,
  "systemFlags": 0,
  "userFlags": 0,
  "totalIndexSize": 0,
  "indexSizes": {
    
  },
  "ok": 1
}

old_collection.js

/*
  SERVER: MongoDB 2.2.0
  NS: tracking.session
*/

/* Before Reindex */
db.session.stats(1024*1024)
{
  "ns": "tracking.session",
  "count": 49650405,
  "size": 50169,
  "avgObjSize": 0.0010104449299054056,
  "storageSize": 51861,
  "numExtents": 46,
  "nindexes": 2,
  "lastExtentSize": 2046,
  "paddingFactor": 1.0000000047677706,
  "systemFlags": 1,
  "userFlags": 0,
  "totalIndexSize": 5048,
  "indexSizes": {
    "_id_": 2313,
    "rt_-1_s_1": 2735
  },
  "ok": 1
}

/* After Reindex */
db.session.stats(1024*1024)
{
  "ns": "tracking.session",
  "count": 49650459,
  "size": 50169,
  "avgObjSize": 0.0010104438309422275,
  "storageSize": 51861,
  "numExtents": 46,
  "nindexes": 2,
  "lastExtentSize": 2046,
  "paddingFactor": 1.0000000047677706,
  "systemFlags": 0,
  "userFlags": 0,
  "totalIndexSize": 3009,
  "indexSizes": {
    "_id_": 1382,
    "rt_-1_s_1": 1626
  },
  "ok": 1
}