It doesn't appear to have been mentioned already but CalDAV and CardDAV support would be almost essential for me so it can be used with ownCloud and/or Apple iCloud. The N9's CalDAV support is ok but it never got CardDAV.

Cisco VPN support.


Apps:

A refreshed port of Web Feeds with support for other RSS sync services since Google are stopping reader - https://projects.developer.nokia.com/feed_reader

A port of SciCalc - http://n9-apps.com/scicalc

A LastPass application and integration with the browser and other apps if possible. LastPass were pretty negative about porting to the N9 when I asked though so I wouldn't hold my breath.

OpenLiveView - http://openliveview.com

Rocket - if the feed integration wasn't so buggy it'd be the best twitter client on the N9 - http://webpointstudio.ru/products/rocket/

An iTunes remote app.