I was having this same question this week due to the refine rebate event. I really don't have a great answer for you. For me, I spent all my low level refines getting all 4 sets of gear to level 4 (125) because I had alot of low level refinements left, and it was easy to buy from the shop with ranked coins I had saved to fini* off.
After that, I tried to focus on the one set of gear that goes on my rusher, or my first slot ninja. My plan was to get all his gear to level up to level 7 (250) until I noticed that level 6 (210) gives the best boost. I can no longer look on the lower level refines (cause all mine is level 4+) but the ones I can see seem to give a plus 40 to each skill. However for what ever reason level 6 gives 45 (level 5 (165) to level level 6 (210)) points instead. So for me, I'll just get all the gear I can to level 6 before moving on.
One other thing I would point out is, I tend to ignore the set on the ninja that does not use their skill at the start of a round (Sasuke, Sasori, Garra and so on) because really the only point in refines (to me) is the initiative, and if your skill simply goes when it is your turn, initiative is not that big of a deal any more. So I save that ninja's gear for last.
Also, to answer Fatesbell's question/comment, it is 100 refine (medium) points from level 6 to 7.