I think your problem is about upgrading from express 2 to 3. In Express 3, most of the package previously bundled with them, are now single package that you need to require, in your app.
Of course you need to include it in your package.json and do the npm install as usual.
var express = require('express')
var session = require('express-session')
var app = express()
app.use(session({secret: 'keyboard cat'}))
See: ExpressJS / Session