In GT4 it was the 787B by a huge margin. I haven't gotten it yet in GT5 but I do have a 908 HDi. I will have to see if my memory of it matches reality and it is better than the 908, but if you can't find the 787 and need a LM/goup C car, the 908 is a good choice.
The Audi R10 TDI. It's not the easiest to drive, to be honest I can't drive it without TC but I love that open cockpit view.
If Porsche was in the game though my favourite would probably be the 911 GT1 '98 Race Car that Alan McNish won his first Le Mans with. I've had a model of that car from when I was 6 years old.
My favourite to drive is the 787b, but my favourite overall is the Bentley. It's probably because I never got to drive it in GT4 and it seems rare online.
The McLaren F1 GTR, it earned respect by its positions from 1995 (1st, 3rd, 4th, 5th and 13th were the positions of all the F1 GTRs in the first year. Amazing right?) to 1998 in Le Mans. Too bad everyone else is forgeting about this motorsport legend..
Since I only need LMP/Group C cars for enduros, my vote is for the R10. Best view for everything off racing. The 787B is a better driving car, and better sounding as well, but it is hard to top the open cockpit view of the R10 streaming down hunaudieres at dawn after three stints in the dark. There is something about the mixed light in the sky, the dark trees and the hints of tailights all open to view that is without equal in this game.
Do like the wind Indy if you have a Red Bull X1, or even better, do the supercar festival season event at Eifel, it takes 4 minutes and earns 190k and is pretty much one of the fastest ways now