EPS, we travel from the North East (Darlington/Northallerton) via York and have always booked trains with National Express East Coast website (used to be GNER until the franchise changed). If you book early enough, then there are good deals to be had, like Wardi said. I think they go on sale for marathon weekend next Thursday.
We also tend to travel down Friday and register to avoid the Expo chaos on the Saturday and then back Sunday night or Monday morning. We stay in Russell Square, but the Travelodge website usually has some cheaper options if you book early enough.
I think most clubs travel this way, unless there are loads of runners entered from a large club, then they make take their own transport. Knavesmire Harriers may be a good club to try, as I know they also marshall at FLM, so make take extra people, if you're looking for company.
Good Luck!!