You say you had 8000 energy?  Is that in your current available?  If so you are wasting energy.  If you are below your cap you accrue free energy at the rate if 1/3 per minute.  That's 480/day that could be used for grinding masteries or gear.

to answer your question I optimize my free energy during a fusion, use daily rewards (440/day at player level 60+), use refills in my inbox, and spend gems as needed. 

• Every day you get 1440/3 = 480 energy just from time, at 3 minutes per energy. Assuming you use all your energy before you go to bed, and you sleep for a "normal" eight hours a night, you'll lose some of that - say, 30 of it. So, you should be able to get about 450 energy per day for free.
• You get one free refill from daily quests and one from advanced quests. You also get 50 free energy from advanced quests. So, that's another 310 energy.
• Every other day you get a free refill in your mailbox. This one, though, is stockpiled over time, so you should be able to maintain a long list of refills to use in a pinch.
• Doom Tower normal and hard both yield significant amounts of energy.
• Tournaments, events, etc all can provide energy as rewards. Same for CvC. These rewards can be stockpiled for about six days usually.
• And then, of course as you mentioned, there are gems, but there's also free refills from clan points.

You missed the refill from playtime rewards lol. But as usual you da man!

Clan shop sometimes or tag Bazaar once a week