This is a performance test of several methods of updating every item in 100000 row MongoDB collection. See comment below for results of test on a small EC2 instance.

mongo_coll_update_test.js

#! /usr/bin/node

var MongoClient = require('mongodb').MongoClient
var Server = require('mongodb').Server;
var async = require('async');
var util = require('util');

// A simple linear congruence random number generator.
// This is anticipating doing a comparable test with the aggregation pipeline.
var randMod = 2 << 24;
var randMult = 1140671485;
var randAdd = 12820163;
function myRand (seed) {
    return (randMult*seed + randAdd) % randMod;
}

// Initial Documents to insert.
var ndoc = 100000;
var i = ndoc;
var docList = [];
while (i) {
    i -= 1;
    docList[i] = {randomVal: myRand(i)};
}

var mongoClient = new MongoClient(new Server('localhost', 27017));
var db = null;
var coll = null;
var anotherColl = null;

var finalReport = '';

// Running all the tests with explicit async.series tasks.
async.series([

    function (dbOpenDone) {
        mongoClient.open( function(err, mongoClient) {
            if (err) {
                dbOpenDone(err);
                return;
            }
            db = mongoClient.db('test');
            coll = db.collection('update_benchmark');
            anotherColl = db.collection('update_benchmark_tmp');
            // db.admin().setProfilingLevel('all', function (plErr) {
            //     dbOpenDone(plErr);
            // });
            dbOpenDone(err);
        });
    },
    
    function (dropDone) {
        // dropDone(null); return;  // uncomment to skip drop
        if (coll) {
            coll.drop(function (err) {
                // Ignore errors from drop.
                dropDone(null);
            });
        } else {
            dropDone(null);
        }
    },     
    
    function (dropDone) {
        // dropDone(null); return;  // uncomment to skip drop
        if (anotherColl) {
            anotherColl.drop(function (err) {
                // Ignore errors from drop.
                dropDone(null);
            });
        } else {
            dropDone(null);
        }
    },            
        
    
    function (insertDone) {
        // insertDone(null); return;   // uncomment to skip insert
        console.log('Inserting docList');
        var iChunk = 0;
        var chunkSize = 10000;
        async.until(function () {return (iChunk >= docList.length);},
            function (insertChunkDone) {
                coll.insert(docList.slice(iChunk, iChunk + chunkSize), function (insErr) {
                    iChunk += chunkSize;
                    process.nextTick(function () {
                        console.log('Finished Insert ' + iChunk);
                        insertChunkDone(insErr);
                    });
                });
            },
            insertDone
        );
    },
    
    // Test Scenario 1: Pull all values onto the client and push them back with individual saves.
    function (testScenario1Done) {
        // testScenario1Done(null); return;   // uncomment to skip testScenario 1
        var description = 'Big find().toArray, and individual saves.';
        console.log('Starting Test Scenario 1');
        var testStart = new Date().getTime();
        coll.find().toArray(function (err, itemList) {
            if (err) {
                testScenario1Done(err);
            }
            console.log('Retrieved all items in: ' + ((new Date().getTime() - testStart)/1000) + ' seconds');
            itemList.forEach(function (item) { 
                item.randomVal = myRand(item.randomVal);
            });
            var i = 0;
            async.forEach(itemList, function (item, itemSaveDone) {
                var checkpointNote = null;
                i += 1;
                if (i % 10000 === 0) {
                    console.log('(1) Saving ' + i);
                    checkpointNote = '(1) Finished saving ' + i;
                }
                coll.save(item, function (err) {
                    if (checkpointNote) {
                        console.log(checkpointNote);
                    }
                    itemSaveDone(err);
                });
            },
            function (err) {
                var elapsed = (new Date().getTime() - testStart)/1000;
                var rpt = 'testScenario1: ' + elapsed + ' seconds';
                console.log(rpt);
                finalReport += rpt + ' (' + description + ')\n';
                testScenario1Done(err);
            });
        });
    },
    
    // Test Scenario 2: Pull all values onto the client and push them back with individual updates.
    function (testScenario2Done) {
        // testScenario2Done(null); return;   // uncomment to skip testScenario 2
        var description = 'Big find().toArray, and individual updates.';
        console.log('Starting Test Scenario 2');
        var testStart = new Date().getTime();
        coll.find().toArray(function (err, itemList) {
            if (err) {
                testScenario1Done(err);
            }
            console.log('Retrieved all items in:' + ((new Date().getTime() - testStart)/1000) + ' seconds');
            var i = 0;
            async.forEach(itemList, function (item, itemUpdateDone) {
                var checkpointNote = null;
                i += 1;
                if (i % 10000 === 0) {
                    console.log('(2) Updating ' + i);
                    checkpointNote = '(2) Finished updating ' + i;
                }
                coll.update(
                    {_id: item._id}, 
                    {$set: {randomVal: myRand(item.randomVal)}}, 
                    function (err) {
                        if (checkpointNote) {
                            console.log(checkpointNote);
                        }
                        itemUpdateDone(err);
                    }
                );
            },
            function (err) {
                var testScenario2Elapsed = (new Date().getTime() - testStart)/1000;
                var rpt = 'testScenario2: ' + testScenario2Elapsed + ' seconds';
                console.log(rpt);
                finalReport += rpt + ' (' + description + ')\n';
                testScenario2Done(err);
            });
        });
    },

    // Test Scenario 3: Iterate on cursor (small batch) and use update.
    function (testScenario3Done) {
        // testScenario3Done(null); return;   // uncomment to skip testScenario 3
        var description = 'Iterate on cursor (size = 10), then update.';
        console.log('Starting Test Scenario 3');
        var testStart = new Date().getTime();
        
        var curs = coll.find().batchSize(10);
        curs.count(function(err, count) {
            var i = 0;
            curs.each(function (err, item) {
                var checkpointNote = null;
                if (err) {
                    testScenario3Done(err);
                }
                if (!item) {
                    return;
                }
                i += 1;
                if (i % 10000 === 0) {
                    checkpointNote = '(3) Finished updating ' + i;
                    console.log('(3) Updating ' + i);
                }
                coll.update(
                    {_id: item._id}, 
                    {$set: {randomVal: myRand(item.randomVal)}},
                    function (err) {
                        if (checkpointNote) {
                            console.log(checkpointNote);
                        }
                        if (err) {
                            testScenario3Done(err);
                        }
                        count -= 1;
                        if (count === 0) {
                            var elapsed = (new Date().getTime() - testStart)/1000;
                            var rpt = 'testScenario3: ' + elapsed + ' seconds';
                            console.log(rpt);
                            finalReport += rpt + ' (' + description + ')\n';
                            testScenario3Done(null);
                        }
                    }
                );
            });
        });
    },
    
    
    // Test Scenario 4: Iterate on cursor (large batch) and use update.
    function (testScenario4Done) {
        // testScenario4Done(null); return;   // uncomment to skip testScenario 4
        var description = 'Iterate on cursor (size = 10000), then update.';
        console.log('Starting Test Scenario 4');
        var testStart = new Date().getTime();
        var curs = coll.find().batchSize(10000);
        curs.count(function(err, count) {
            var i = 0;
            curs.each(function (err, item) {
                var checkpointNote = null;
                if (err) {
                    testScenario4Done(err);
                }
                if (!item) {
                    return;
                }
                i += 1;
                if (i % 10000 === 0) {
                    checkpointNote = '(4) Finished updating ' + i;
                    console.log('(4) Updating ' + i);
                }
                coll.update(
                    {_id: item._id}, 
                    {$set: {randomVal: myRand(item.randomVal)}},
                    function (err) {
                        if (checkpointNote) {
                            console.log(checkpointNote);
                        }
                        if (err) {
                            testScenario4Done(err);
                        }
                        count -= 1;
                        if (count === 0) {
                            var elapsed = (new Date().getTime() - testStart)/1000;
                            var rpt = 'testScenario4: ' + elapsed + ' seconds';
                            console.log(rpt);
                            finalReport += rpt + ' (' + description + ')\n';
                            testScenario4Done(null);
                        }
                    }
                );
            });
        });
    },
    
    // Test Scenario 5: Iterate on cursor (large batch) and fill a brand new collection.
    function (testScenario5Done) {
        // testScenario5Done(null); return;   // uncomment to skip testScenario 5
        var description = 'Iterate on cursor (size = 10000), then update.';
        console.log('Starting Test Scenario 5');
        var testStart = new Date().getTime();
        var curs = coll.find().batchSize(10000);
        curs.count(function(err, count) {
            var i = 0;
            var newDocList = [];
            curs.each(function (err, item) {
                var checkpointNote = null;
                if (err) {
                    testScenario5Done(err);
                }
                if (!item) {
                    return;
                }
                item.randomVal = myRand(item.randomVal);
                newDocList[i%10000] = item;
                i += 1;
                if (i % 10000 === 0 || i === count) {
                    checkpointNote = '(5) Finished updating ' + i;
                    console.log('(5) Updating ' + i);
                    anotherColl.insert(newDocList, function (err) {
                        if (checkpointNote) {
                            console.log(checkpointNote);
                        }
                        if (err) {
                            testScenario5Done(err);
                        }
                        if (i === count) { 
                            var elapsed = (new Date().getTime() - testStart)/1000;
                            var rpt = 'testScenario5: ' + elapsed + ' seconds';
                            console.log(rpt);
                            finalReport += rpt + ' (' + description + ')\n';
                            testScenario5Done(err);
                        }
                    });
                }
            });
        });
    }
],
function (err) {
    console.log('\n\nFinal Report:\n' + finalReport);
    mongoClient.close();
    if (err) {
        console.log(err);
        process.exit(1);
    }
    process.exit(0);
});

Here are the results running on a small EC2 instance with the MongoDB at localhost.

• testScenario1: 108.661 seconds -- Uses find().toArray to pull in all the items at once then replaces the documents with individual "save" calls.
• testScenario2: 99.645 seconds -- Uses find().toArray to pull in all the items at once then updates the documents with individual "update" calls.
• testScenario3: 74.553 seconds -- Iterates on the cursor (find().each) with batchSize = 10, then uses individual update calls.
• testScenario4: 58.673 seconds -- Iterates on the cursor (find().each) with batchSize = 10000, then uses individual update calls.
• testScenario5: 4.727 seconds -- Iterates on the cursor with batchSize = 10000, and does inserts into a new collection10000 items at a time.

Though not included I also did a test with MapReduce used as a server side filter which ran at about 19 seconds. I would have liked to have similarly used "aggregate" as a server side filter, but it doesn't yet have an option to output to a collection.