The Ireland-Northern Ireland cross-border programme is managed by the Special EU Programmes Body (www.seupb.org), which is a joint cross-border body set up by the British-Irish agreement of 1999 especially to run this type of co-operation programme. They also run the Peace and Reconciliation programme, which runs parallel to the cross-border programme and is focussed on bringing the different communities in Northern Ireland and the border counties of Ireland together.
Both programmes are undergoing changes with the new programming period. The cross-border programme will now include areas of South-West Scotland, as a result of the widening of the definition of "maritime cross-border". This offers extra opportunities for co-operation on tourism, transport and environmental issues and is causing much excitement in Scotland (see declaration of the Irish Taoiseach and the (previous) Scottish first Minister here - http://www.scotland.gov.uk/News/Releases/2006/11/13165243). Meanwhile, the PEACE programme will now be a cross-border programme, legally speaking, rather than a regional development programme. This will offer some extra challenges for co-ordination between the two programmes, as well as meaning that project partnerships will have to be constructed quite carefully.
The SEUPB website is well presented and laid out, although navigation at times could be more straightforward. There is evidently so much experience to glean from the two programmes, but extracting it from the web is sometimes problematic. An example of this is the rumours I have heard about a conference in early October to publicise the success of the PEACE programme for other parts of the world facing similar challenges (Cyprus, the Balkans, the Middle East). A great idea, I hope all will agree, but it is impossible to find anything on the website at present. I will keep watching.