As a note, nearly all the times provided to you by the game (And Plarium) will be in UTC. You can read more about it here ( https://en.wikipedia.org/wiki/Coordinated_Universal_Time ), and can convert your current time zone into UTC time to match it up here ( http://www.timeanddate.com/worldclock/converter.html ). 
This is also intended for players that are new to the game (Usually less than 3 months), though more experience players may find this guide of some use as well.

Daily Reward Roster
This little calendar shaped-icon left of your combat adviser will notify you of how many days you have consecutively logged into the game. When you click on it, it will give you the chart of what rewards you get on which days of your log in streak, which can provide some motivation.

Daily Discounts
Every 22 hours, you get a special discount on in-game items, whether they be purchased with Crystals or real-world currency. They can be up to 80% off, and can be discounts for nearly everything in the game (Defensive troops, offensive troops, fleet battle groups, serum boxes, Echelon activators, etc.). You can also see your current discount in your Black Market tabs and choose which discounts to take advantage of. 

Colonies
Invading and occupying colonies is task that can be very difficult, especially if the owner of said sector is active. Logging in and collecting the accumulated resources will maximize your profit, especially as you can only hold 12 hour’s worth of resources (Regardless of how many resources per hour your colony produces). 

Raids
Your raid points increase by 1 every 2.5 hours, or just under 10 times every day. You can also raid up to 100K from a single sector at a given time, and have a maximum of 10 raid points at any given time. Given these 3 factors, you can raid up to 1.9M resources a day. All of this can be checked by mousing over any sector that is not your own. The massive possible resource gain is why you want to log in and use your raid points. 

Spending Resources
On the topic of forcible exchanging of resources, you want to prevent such occurrence from happening to yourself. While you can stack your sector with defence troops and other defensive items, your best protection is not presenting any resources to your attackers at all, and keeping your resource total as close to 0 as possible when you’re inactive for a long period of time. 

Bunkering Troops
While you’re preventing your resources from being stolen, you may also want to prevent your troops from being stolen. (Well, not literally stolen.) But you will still lose troops if there are any unbunkered while a successful attack happens, which is why you want to log in frequently to remove your troops from your possible predators’ sight, via the bunker. 

Clan Reward Packs/Missions
This requires your membership in a clan. You and your clan (if applicable) will be assigned missions, which can range from training troops, to raiding for resources. You will want to log in, and pull your weight for the clan. 
When your clan reaches certain amounts of points, you will receive reward packs, which are small but useful bonuses. However, they disappear after 72 hours of being earned, so they will need to be monitored regularly and frequently. 

Clan Antigen Privileges
This requires your membership in a clan, and an Emitter held in your clan’s name. This may also require you to have a certain amount of defensive troops stationed at the Emitter, and certainly requires your troops at the Emitter. 
Most clans reward their members’ defensive participation with Antigen. Morgana’s Mutants visit the Emitters a couple times a day, and if your clan successfully defends your Emitter from her Mutants, you and your clan will be rewarded with Antigen, which is added directly to your Emitter that was attacked and defended . Clan Leaders and Deputy Clan Leaders can decide who to allow Antigen usage to, and they will usually do so on a timed basis, and will usually do so on the specific span of a day. To maximize your profit from the situation, you will need to log in daily to be sure you can use all your allotted Antigen. 

Cyborgs/Research
You can create a default maximum of 3 of the useful, upkeep-free units a day, Cyborgs. If you have purchased Mutagen Barrels, you will only be losing out more by not logging in and creating your Cyborgs. 
You can also visit your friends’ sectors, creating Cyborgs for them and helping them research their modules, and in turn they can return the favour. 

Free Resource Canisters
While you visit your friends’ sectors, you may also notice resource canisters around their sector, which will give you free resources when clicked. The amount given will vary on your appropriate mine/vault levels 

Daily Missions
You are given missions with varying goals that last 4 hours long, once you finish/collect the rewards of your previous mission. These missions are found directly underneath your tournaments 

Weekly Rankings
Starting every Monday morning, the weekly rankings are awarded and reset, allowing the highest performing players in certain categories to receive rewards for their effort. However, this requires dedication and hard work, which coincidentally usually requires logging in every day as well. 

Concluding
So now that you know how you can maximize your daily rewards by taking at least few minutes a day to log in, you can give yourself an edge even over some veterans who may not have time to manage their sector 24/7. 

Let me know what you guys (Newer players and veterans alike) think of this guide, such as how I could improve on it, and possible ideas for me to cover in the future. I am open to all constructive criticism :)