They are all good engines but here are my thoughts:
1st Cummins . Large population of engines. If you should ever need a replacement engine or parts, the Cummins will cost considerably less than any other brand.
2nd Perkins, Cat (same thing "Perkapillar")The best product support network in the world.
3rd John Deere. The product support of a Cummins at the price of a Cat.
Stay away from Duetz, Isuzu, Fiat (FPT) Scania and any other "exotics". They are good engines until you need product support.
These are generalizations. A good dealer close by changes everything. Some engine models within the same manufacturer are better than others. For example, some engines models had a production life spanning 20-30 years. Other 4 years(due to changing emissions requirements). The engine with a longer production like would be more desirable. An engine that I used to sell new for $4500 in 2001 no longer available new. It has been replaced by three different generations of engine design in the last 12 years, no longer available as a new replacement engine, cost $13,500 for a remanufactured engine plus a $4000 core.
That older equipment is looking like better deal everyday.