Unless you intend to spend money on this game, farming is absolutely essential in this game. There are several key resources.
Currently, best way to obtain this seems to be flight missions or normal missions or pvp, depending on how often you log in. For flight missions, 20 minute flights are the most rewarding by far, giving more silver per minute on average than any other time.
Similar to the Command Points farming below, one known method to farm Command Points is to relaunch Chapter 1, Assignment 3 and complete the first task repeatedly. Task 1 requires you to complete 3 Flight Deck missions. The shortest Flight Deck mission is 3 minutes (Flight Deck Jets level 1 and 2), or 10 minutes (Flight Deck Jets level 3+). As soon as this has completed, collect the silver to complete Task 1, which is 900 silver. This means it's possible to make between 15k-20k per hour with three 3-minute Flight Deck Jets and resending the jets within a minute of completing their flight.
Conversely, you could do 20 minute flights, but even with the highest level jets piloted by the highest level heroes, you're only going to make about 2500-3000 silver with 3 jets and the mission bonus every 20 minutes, or less than 10k an hour, although it is easier to continue playing missions and attacking bases while doing 20 minute flights.
Can be collected either from completing missions, raiding enemy bases, or raiding other players' bases. You can also collect it from your Iso-8 refinery, with the amount and time taken to reach 100% increasing the more you level up your base.
Once rare and impossible to get in previous versions, currently VERY easy to get, since you can send and receive 25 gifts a day, AND it is not limitted per neighbour, so you only need to cooperate with 1 neighbour to get your 25 a day. You also get 1 from each ally on ally bar a day.
One known method to farm Command Points is to relaunch Chapter 1, Assignment 3 and complete the first two Tasks of the assignment repeatedly. Task 1 requires you to complete 3 Flight Deck missions. The shortest Flight Deck mission is 3 minutes (Flight Deck Jets level 1 only), or 10 minutes (Flight Deck Jets level 2+). As soon as this has completed, collect the silver to complete Task 1. Task 2 is a battle against Viper, Power Armor and guards. You will have to defeat all enemies to complete the mission. The Power Armor can only be attacked after Viper is defeated (you just have to drastically reduce her HP and she'll flee). Once you beat this Task you get your reward and gain access to a reward spinner that has a 30% chance of awarding Command Points (1, 3, or 5CP).
As soon as you've collected the silver from the flight deck, immediately send the jet out again on the same mission. This means that by the time you've finished the fight against Viper and Power Armor, you can reset the assignment and instantly complete Task 1.
If energy consumption is not a problem for you,and you don't mind spending an extra of 20 energy on this assignment, you might want to play the whole thing over and over again. As out of the 5 missions only 3 require energy (the other two are a flight deck and a silver gathering tasks), this method is still well paced, and you have chance to get CP from two spins (one roulette after defeating the Viper/Power Armor mini-boss, and one after Red Skull), furthermore you will get that 1 CP for sure for completing the assignment.
Currently, leveling up your Commander is the only way to obtain additional Gold without paying for it. Re-launch and complete missions to gain XP. Best mission is unknown.