I have a 88 XJ and most of the joints have grease fittings. Like you have discussed the ones without fittings are the lower ball joints and the front axle shaft u-joints.
I asked my driveshaft shop about the lack of grease fittings when I was picking up new u-joints for the axle shafts. The owner told me if you can get grease into it then the water can wash it out. If you take it your XJ will be fording creeks then sealed lower ball joints and axle shaft u-joints makes perfect sense.
Here some tips my Dad told me back when I was a teenager. You need to wipe the dirt off the grease fitting then hook up the grease gun and pump in the grease. Also pump until you see new grease coming out of the joint. Some people say pump until you hear the "pop" sound then stop. That means you just pushed air out of the joint but I have not seen any grease coming out. When you pull off the grease gun leave the grease film on the fitting to protect it from rusting.
Another tip from my Dad is to have the weight off the suspension when you lube the front suspension. That way you can get fresh grease into the area normally in contact, like on a U-joint. I am lucky I have use of a lift to change my oil, I can lube the entire suspension with the weight off the suspension.
You will need a needle fitting to lube the double cardin joint on the front driveshaft. The fitting looks like a plug but you do push the needle into the fitting and it should take grease.
Most people just use what ever grease is in the gun. I have a dedicated gun for my XJ and I keep it in a plastic tools box just incase the liquid leaks out of the gun. I have a grease gun that looks like this:
http://www.northerntool.com/images/product/images/403899_lg.jpg This allows me to hold the connector on the grease fitting with one hand and operate the gun with the other hand.
When I installed the front axle u-joints I did some reseach on grease and concluded to use the valvoline fully synthetic grease. I had been using Mobil 1 grease but the fully synthetic valvoline had a wider temperature range. I figure spend $4.50 for a tube of grease instead of $2.00, just cheap insurance.