Mongoskin is not helping with the issue either, since it's not even maintained anymore.

Even defining replica sets separately in the config result in:
MONGOSKIN:WARN: database or username found in RepliSet server URL, user:pass@xxxx.candidate.xx.mongolayer.com:port/countly

In most cases this should not be an issue, because Countly provides mongoskin version which has older mongodb driver with it and you should be able to connect to same mongodb by using older url scheme (without mongodb:// protocol), which should look like this:

var countlyConfig = {
    mongodb: "foo:bar@d1.mongolab.com:39530/countly?auto_reconnect=true",

Have a test server set up which works with Mongodb 2.6.6

But it most probably won't work with multiple hosts

The other option is to upgrade mongoskin to higher than 1.3.20 (I think the latest one is 1.4.4) that will also upgrade mongodb driver and ability to use new connections urls. I'm now testing on test server and it seems to be working ok, only changes needed to be made is using new url scheme in both countly configs:

var countlyConfig = {
    mongodb: "mongodb://localhost:27017/countly",

And only difference seems to be that SkinClass does not have ObjectID method, so need to add little hack to /api/utils/common.js

after common.db = mongo.db(dbName, dbOptions) need to add

    if(!common.db.ObjectID)
        common.db.ObjectID = mongo.ObjectID;

and in /frontend/express/app.js after var countlyDb = mongo.db(dbName, dbOptions) need to add

if(!countlyDb.ObjectID)
    countlyDb.ObjectID = mongo.ObjectID;

So far it seems to be working and we could switch to new driver in new release

Thank you for the testing and the patches!

I'm very much looking forward to proper multi-host connection string support, and I'm sure that a lot of others are as well.

Hmm, but using replSets also seem to work, if you do not use db name in each server like:

mongodb: {
        replSetServers : [
            'd1.mongolab.com:39530',
            'd2.mongolab.com:39530'
        ],
        db: "countly",
        max_pool_size: 1000
    },

That's what I tried in the second comment, but I additionally had to add a username & password. I tried setting the database name with the URL and without it in the URL but in the db variable instead, neither worked and produced the warning in comment number 2.

I'm trying to use Compose.io again as the DB host. What roles does Countly require from the database user?
Compose.io gives readWrite@db, but not dbAdmin@db, and I'm seeing these in the MongoDB log file:

assertion 13 not authorized for query on countly.members ns:countly.members query:{ api_key: "" }

Yeah, it's not a permission issue, it's an issue with Countly/MongoDB driver.
It would seem like there's no username & password support for when using replSetServers.

New MongoDB driver (including new connection string format) is used in b657d76