To add to what Skadi has already mentioned, there is a natural energy regeneration per day that people who keep their energy at 0 are able to benefit from.
But in addition to that, there are other areas such as:
- Classic arena tournament rewards (150 energy per tournament, every second week)
- Tag team tournament rewards (300 energy per tournament, every second week)
- Clan shop (1000 energy every second week. There's a 50/50 chance of energy or chickens in the clan shop each week, so you might get 4 weeks in a row of 1000 energy, or you might get chickens, but it averages out)
- Artifact enhancement events also provide energy at low spend. You can just take a few artifacts to level 12 for minimal silver cost and get the energy rewards. I think you can get about 150 or so, every 2 weeks
- Daily logins - At the 270 day repeating you can get 1000 energy a month. Prior to the 270 day though it is a bit more random, but every month has energy in it. For example, in the 60 day bracket there is 2000 energy. In the 90 day bracket there is 2500 energy
- The playtime rewards that reset each day has a full energy at 60 minutes
- The free gift from the shop also provides a full energy refill. This usually cycles out every second day or so. Note that for these will go into your inbox and have a 99 expiration timer on them. It is usually better to keep these for emergencies
- Once you start progressing in doom tower, you will start to get consistent energy rewards every 10 floors
- Fusion Warmup event which happens once a month also has a batch of free energy for cheap, even if you don't plan on doing the fusion event.
There are other non-reoccuring energy sources as well, including promo codes that usually have energy and are released sometimes once a month, plus free gifts for holidays or anniverseries. Early game, you will get a lot of energy from missions, challenges, Campaign rewards and Faction Wars rewards.
I feel like I am missing some sources, and while each individual source isn't much they do add up. I am usually busy with work during the week so I do the bare minimum, and by the end of the week I have usually accumulated a decent 3K energy from passive playing.
I also don't use gems much anymore, so I have about 12K gems sitting there doing nothing, which I could use to buy full energy refills if I really need to.