Q:
I know that that the XONE:2D is not "Traktor Scratch Certified" hardware, so cannot be used with Traktor Scratch Pro.
Which other virtual DJ applications that use timecode CD/vinyl can be used with the XONE2D?

A:
There are various virtual DJ packages that can support encoded vinyl without a proprietary licensed hardware interface;  in general, check for apps that require an ASIO soundcard and RIAA (phono) preamp only (the XONE 2D includes both).

At the time of writing, here are two we are aware of which you can use timecode media and the XONE:2D:

DJ Decks offers timecode vinyl control compatibility, using other software designers' encoded vinyl.
They also provide information on configuring the XONE:2D interface and MIDI mapping the device.
Find more info about this via their website:
http://djdecks.be/index.php?module=docs&sub_help=allenheathxone2d.php
http://djdecks.be/index.php?module=docs&sub_help=vinylcontrol.php

Virtual DJ Pro
http://www.virtualdj.com/products/index.html

NOTE:
It’s always worth double-checking with the software designers via their customer support team for info on hardware compatibility, or browsing their user forums for more details, before committing to the purchase, but both of the above should offer you alternatives to Native Instruments Traktor Scratch Pro, or Serato Scratch Live, both of which require licensed hardware interfaces.

If you plan to use Traktor Scratch Pro in particular, but want to use Allen & Heath hardware, the XONE:4D is a fully 'Traktor Scratch Certified' interface and fully compatible with NI’s timecode media.