Because diesels compress roughly twice the amount that gasoline engines compress, they are harder hit by altitude.  Because all engines need air to burn gasoline or oil, all engines are affected by altitude. The most common estimate is that: (from http://www.pickuptruck.com/html/history/segment12.html)

"A non-turbo diesel loses 3 percent of power for every 1,000 feet of altitude. At 10,000 feet the V-8 lost about 30 percent of its power, the Cummins turbodiesel [as an example of the standard naturally aspirated diesel] lost only about 5 percent."

Because the amount of oxygen at 6000 feet above sea level can be estimated at roughly 1/3rd of the amount of Oxygen, needless to say diesels can be effected heavily by altitude.  On a 3B or 2H light altitude, say, 3-4000 feet can produce excess smoking.  On these engines the easiest solution is to turn down the fuel which is a simple little screw in the EDIC Control.  Furthermore, excess fuel especially at altitude also produces extreme exhaust gas temperatures which can damage your engine.

When I arrived in Salt Lake City from Out East, my HJ60 smoking pretty badly and I had a fairly significant loss of power.  So I got on the DTLC and was told to have my injectors rebuilt.  So, I spent about $600 having them rebuilt, and it made no difference with smoking but did produce a light increase in power.

Turning down the fuel was the ultimate change in power. 

2H and 3B engines, producing approx 100hp and 170 ft/lbs of torque, are "weak enough" engines that altitude will take a normally seemly somewhat powerful truck and make it a slug. 

1HZ models I'm told aren't affected by altitude until they reach above 7,000 feet but I personally believe because they have a little more all around power, their engines still have the ability to produce adequate acceleration and general power despite the lack of oxygen.  This is because I cannot understand how altitude cannot affect naturally aspirated engines with the same relative RPM range, and number of valves.

The only solution to combat you engine's lack of performance in altitude is to turbocharge.  You can also reduce your axle gearing to allow your engine to turn your tires more easily.  Furthermore, larger tires affect a diesel's lack of power greater in altitude.