Our guild uses one DKP system only, and it applies to all 40-man raids. We are currently running MC, Onyxia, BWL, and AQ40 on a weekly basis, so the same totals are used for all 4 places. I think this works out for us because we are a small guild (only 38 members) and don't have that many people to keep track of.
Our 20-man raids don't use DKP at all, we just collectively decide who should get the items, or we free-roll them off. Again, I think this works well for us because we are a small guild whose members know each other pretty well and loot is usually not an issue.
I have heard of larger guilds using one DKP system for 40-man raids and one for 20-mans. I've also read about guilds that use a different DKP system for each instance...but I think they have either lots and lots of members or too much time on their hands.