I have been in the US on a H1B visa since the beginning of 2012 and need to file my taxes. I am married but my wife, who has got a H4 visa is still in the UK - do I file jointly or does my wife actually have to file despite not being in the US?

You can file jointly; your wife's location is irrelevant.

She has to sign the return AND probably the Form W-7 for an ITIN, but that can be done; it just takes a bit of time.

If you believe that you will need professional help filing this year, this IS what I do. Please double-click on my name (Atlanta Tax Expert) above to access my profile. You will find my email address in the signature portion of the profile (scroll down to the BOTTOM of the page).

You file joint return as residents. You will attach W7 (ITIN applicatin) with your tax return. You must both report your worldwide income.
You must both declare your worldwide income for 2012. If you have any foreign income, and on that income you paid taxes in the foreign country, then you can claim foreign tax credit (Form 1116).