No major differences.   I would avoid the Cat C9 engine since it was underpowered compared to the Cummins ISL and only used a couple years in motorhomes so they had trouble mating it with the Allison transmission.  But if the motorhome you find is a real deal make sure you have both the C9 and Allison computers revved to current levels and you should be fine.  C7 and C11 Cat engines have been commonly used in motorhomes, so don't worry about them.

Avoid Mercedes engines, they are built more for light duty than heavy duty. A diesel mechanic once told me if you accidently put gas in a Cummins, Cat or Detroit Diesel engine then you take it apart, clean it, replace the gaskets and it will run like new.  If you put gas in a Mercedes diesel you throw it in a dumpster

Cat and Detroit Diesel bet on fancy engineering to get their engines working for the 2010 emissions without a urea tank and lost the bet. Since they have no engines that can meet the standards, they can't sell them for trucks and motorhomes. They will both be back in the over the road engines eventually, probably with urea tanks, there is just too much money to be made to stay out of it. Parts and service are no problem since both companies are in business and there are lots of engines out there.

All diesel engine manufacturers were looking at the 2010 emissions rules as a way to make money because they figured on selling lots of new engines so they did not put up a fight over the rules.

Edit: I mentioned Mercedes since some Freightliners Class A chassis have them inculding the late model Alfa See Ya Founder edition.  Bus conversions and high end motorhomes sometimes have Detroit Diesels.  Some new motorhomes might come with Navistar engines, the same company that made the lousy 6.0, so I don't trust them to be good engines.

-- Edited by bjoyce on Tuesday 22nd of February 2011 11:01:32 PM

"Bus conversions and high end motorhomes sometimes have Detroit Diesels." I've been researching Wanderlodges, and that seems to be true of them. How are they, especially those of the late 90's? From what I'm reading on their forum, they seem to be getting 8-9 mpg @ 60 mph.