For longarming, my favorite thread is Bottom Line in both top and bobbin. It is a very fine thread and makes my free-motion quilting look better than it actually is! Before I discovered Bottom Line, I thought I would always use Glide. It is heavier than Bottom Line with a little shine to it, which gave my quilts some sparkle. It shows up more than Bottom Line, for sure. Both are polyester threads, which I far prefer over cotton threads in my machine (a Voyager 17).
I tried cotton thread in my first quilts, including King Tut. It was fine until I tried Glide. I much prefer polyester thread because it leaves much less lint in my machine, plus it is stronger and less likely to break. Also, I like to quilt closely. Close quilting with a heavy cotton thread such as King Tut adds some stiffness to the quilt. Similar quilting with a polyester thread adds no stiffness at all, so the quilt stays very soft.
Threads, as with everything else involved in quilting, is a personal choice. Some quilters here have mentioned using serger thread in their longarm and been perfectly satisfied with it. I would not use serger thread in my machine for a couple of reasons. One is that it is very linty. Another is that it is a relatively weak thread that would break in my machine (former owner told me she struggled for months because she had been told she could use any thread in it). For me, the lint and breakage are just not worth it.