Boy oh boy... 
BTW, you probably know this, but Dodge started putting the Cummins in their truck in the 1989 model year. The "First Generation" was around until '93. In '94, they changed to the newer bodystyle, and also made some engine improvements (inline injector pump instead of rotary, a bit more horsepower, etc). '89 and some '90 trucks did not have intercoolers, and some early trucks were equipped with 3 speed automatics, which were bulletproof but offer no overdrive gear.
Ford started putting the 6.9l Navistar engine in their truck in '83. Halfway through the '87 model year, they started using the 7.3l instead. They kept the IDI 7.3l until halfway through the '94 model year when they switched to the Powerstroke. Some '94 IDI's have factory turbo's; otherwise, every engine came from the factory naturally aspirated. Note that, except for the turbo'ed IDI's, the 6.9l and the 7.3l put out almost the exact same power numbers (the 6.9l puts out 175 horsepower and 300 lb-ft of torque; the 7.3l puts out 185 horsepower and about 325 ft-lbs of torque).
Dodge:
Good: - The 6BT Cummins is nearly indestructible if you treat it right; I would put it on par with the OM616 as far as reliability goes (more than one example has made it past 1 million miles)
- Except for the '89 and some '90 trucks, every version is available with an overdrive gear
- Excellent fuel mileage; if you drive easy and have 3.54 gears, some people have seen almost 20mpg
- They just plain sound mean, especially if you straight-pipe it (since it's turbo'ed, doing so is probably legal too
 )
- The inline-6 design makes for a relatively uncluttered engine compartment
- If you decide you don't have enough power, the engine isn't too difficult to modify
- Solid front axle on all 4x4 models; easier to keep aligned and more rugged
Bad: - '89-'93 used a Getrag manual transmission, which has a limited lifespan (it's not difficult to swap an NV4500 in, though, and the NV4500 is indestructible {note that '94+ trucks use the NV4500 instead})
- On '94-'98 12 valves, there is a dowel pin in the timing gear housing cover that can fall out into the gears, causing severe damage. This problem is acknowledged by Cummins (and was corrected on later engines), and a permanent fix is not difficult to do. I don't know if '89-'93 trucks have this issue.
- Fewer of them were built, so they're harder to find, and for that reason (and due to their longevity), the price for one is typically a couple of thousand higher than for a Ford of the same model year
Ford:
Good: - Easier to find; Ford's been making diesels since '83 while Dodge started in '89; for the same reason, there's more of them and they typically come cheaper.
- The Borg-Warner T-19 4 speed manual transmission (used from '83 to '87) is just about indestructible
- The Ford C-6 3 speed automatic (used between '83 and '88) is also just about indestrucible
- The bottom end is very stout
Bad: - CAVITATION!!! This mainly pertains to the 7.3l IDI. There is a coolant additive that needs to be properly maintained in the antifreeze. The good news is that, with the additive, you're pretty much home free. The bad news is that nearly no one knows about it. To make a long story short, if the additive is not used, pinholes develop between the cooling jacket and the rearmost two cylinders, eventually (usually in 200K to 250K miles, but it has been known to happen sooner) hydrolocking the engine and requiring you to resleeve the whole thing. If you look at a 7.3l IDI, ask the owner if they've been using FW-16. If they look at you blankly, don't buy the truck unless it has less than 100,000 miles on it. The chances of doing a rebuild (or a short block replacement) are just too high.
- Injector pumps. There's a nylon gear in the Stanadyne rotary pump that has a tendency to start dissolving, rendering the pump useless. The pumps typically last about 100,000 miles, and the cheapest replacement costs about $300. Also, the fuel injectors are not of excellent quality; you almost never hear of people replacing injectors on M-B's, but doing so on either Ford IDI is not all that uncommon.
- Block cracking; on engines built prior to midway through '85, sometimes a crack forms in the block near the block heater. Using the heater makes this worse. This is an admitted problem, and blocks made after a certain serial number (I don't remember the exact number but it's roughly midway through the '85 model year), this part was redesigned and no longer poses a problem. If the block cracks, you'll be losing coolant out the side but engine operation won't be affected otherwise.
- The E4OD (4 speed overdrive auto used from '89 on up) is a piece of junk!!!!! If you find a good rebuild shop, they can be rebuilt to be stronger (better clutch packings, firmer shifts so the clutches aren't put under so much stress), but unless the truck's going to be running around empty all the time, I would plan on rebuilding it at least once, unless it's a fresh rebuild.
- No overdrive available with a 6.9l unless you get very lucky (a very few 6.9l's were equipped with 5 speeds in '87) or an auxiliary transmission was installed. With 4.10 rear end gears, this means that the engine'll be screaming on the freeways.
- Independent front suspension used on all F-series trucks up to '85, and on all F-250's up to...actually, '97. This axle is prone to alignment problems, and can often eat up the tire on one side without doing much to the tire on the other side. But, if you know a good alignment shop and if the front suspension has been taken care of, it shouldn't be a big issue.
- Glow Plugs. This is an annoyance more than anything else, but on '83-'86 trucks, the electronic controller for the plugs has a tendency to go out. It's best to bypass the controller entirely and mount a switch in the cab to trigger the power relay that actually gives the plugs juice. The controller often fails "On", and Ford in their infinite wisdom uses 6 volt plugs with 12 volts applied to them, so they burn out if left on longer than 10 seconds or so.
I think I got everything...if you can afford it, my vote goes to Dodge. I actually want to put a 12 valve Cummins in my truck someday. However, in spite of that list I wouldn't call the Ford a bad truck. There are some engine issues, but if taken care of, they can last a while. I've got 215K miles on my F-250, and while that may not be that high by MB diesel standards, that's still amazing compared to an '84 Ford 460-powered truck. I also get 15mpg.
One last suggestion would be to get a truck with 3.54 differential gearing. I've owned both, and especially 'cause these diesels don't really care for high RPM's (the 6.9l and 7.3l hit the governor at 3400 RPM, and the Cummins even lower), IMHO the trucks are more flexible with 3.54 gearing. With my 4.10's and 4 speed, I"m in top gear by 35 mph. 
Hope that helps some...you might also want to check out www.thedieselstop.com (Ford) and www.dieseltruckresource.com (Dodge). If I can be of any further help, let me know. Good luck with your decision!
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