I find that the freshly cut thread, as it comes off the spool, is the easiest to thread. The other end seems to fray out, depending on the thread of course. I also believe that if you are hand sewing (quilting, binding, whatever) that the thread does not twist up as much if you keep that thread in the correct direction as it goes through the fabric over and over (the direction that it came off the spool). Therefore, as soon as I thread a needle I put a knot on the trailing end so I know what the leading end is. If I don't need the knot, I just cut it off as necessary.
On the other hand, whatever is easiest to thread and sew with is what is best.
I hope this helps.
Aileen