I've spent a lot of time over several jeeps analyzing what leads to a good ride and I've come to the following conclusions which isn't a parts list so much as a build philosophy.
1) Ride Height. Lower = Better from a comfort standpoint for two primary reasons. First, flatter control arm angles which have been discussed to death on every forum. Second, picture your jeep from the side with a triangle superimposed on it. The two lower corners of the triangle are your front and rear hubs and the top corner is your butt. Now, imagine your jeep going through an endless series of whoops and pitching back and forth. The higher your butt is the longer the legs of the triangle are and the more exagerrated the fore/aft pitching you are going to experience. This theory also works from side to side.
2) Unsprung/Sprung weight ratio. Heavy axles, tires, and wheels are going to make your jeep ride worse than lighter ones if the rest of the jeep weighs the same. So spend a few extra $$ on aluminum wheels and either beef up your existing axles or spring for a custom 609/9" set before you throw those heavy 60s under there. You could also make your jeep ride better by increasing sprung weight, but I still try to keep my jeep as light as possible because lower overall weight will make it stop/go/turn better and they seem to get heavy all on their own anyway.
3) Triangulated three/four link out back. Get rid of the rear panhard with this suspension setup. Ever pulled up a curb and had your head do the side to side head swing? That's the rear panhard which runs opposite of the front panhard. Unless your going full hydro you can't get rid of the front, so triangulate the rear and get rid of the panhard back there. A panhard is sometimes also called a track bar by jeep guys.
4) Wheelbase. As long as you are getting rid of the rear panhard and triangulating, stretch the rear. On an LJ, just drop the tank, cut out that rear brace, and bolt the tank in the stock tj location 5" further back. Then move your axle. You're basically putting the rear tires and tank in the same spot as a tj in relation to the rear of the jeep. Increasing the wheelbase has an effect similar to lowering the jeep as far as the hub/butt triangle we discussed earlier goes (again, increasing tract width also helps similarly). It will decrease your break over angle, but your departure angle will be better. And it's a big job, but doing that and getting rid of the panhard back there will yield ride comfort
dividends.
5) Up Travel. The more up travel you have jn your suspension before you encounter bump stops, the more your suspension can soak up the bumps before they get to your butt. Ideally you want to keep your ride height low, but have a bunch of uptravel. The more of a fabricator you are, the more you can get. I think 4" is minimum and 6" is better.
Other than this it's a matter of tuning your spring shock combo. If you are willing to go the extra mile, run a suspension frequency calculation to determine ideal spring rates at each corner for your particular jeep. Coil overs are awesome from a tune ability standpoint. I may try ORIs is spring which have a packaging advantage because they are shock/spring/swaybar/bump all built into one.
Hope this isn't too overwhelming, but the geometry I talked about makes way more difference than which off the shelf spring/shock to use all of which are compromises of varying degrees.