All Daily Bonuses reset at 12:00 AM local time.
The first Pokemon you catch each day will reward an extra 500 XP and 600 Stardust. If you do this for 7 consecutive days, the 7-Day Catch Streak Bonus will reward you with an extra 2500 XP and 3000 Stardust.
The first Pokestop you spin each day will reward an extra 500 XP and a minimum of 6 items. If you do this for 7 consecutive days, the 7-Day Spin Streak Bonus will reward you with an extra 2500 XP and a minimum of 28 items, along with one of five evolution items: Sun Stone, King's Rock, Metal Coat, Up-Grade, and Dragon Scale. Sinnoh Stones are NOT obtainable from Pokestops.
Raids are the most consistent source of highly-desirable items like Rare Candies and Charged TMs. If possible, you want to do Tier 5 Raids, as they give out the most items, and you want to do them in small groups of 5 or less to maximize your rewards.
If you missed yesterday's Raid, you can carry that Raid Pass forward to today; just make sure you pick up today's Raid Pass afterwards
Once a day, completing a Field Research Task will grant you a Research Stamp. Collecting 7 Stamps will reward you with a Research Breakthrough, which is a fancy way of saying you get 2000 Stardust, 3000 XP, some items, and an encounter with a Level 15 Legendary. The Legendary Reward changes every few months; for the current Research Breakthrough, see here.
This is very dependent on where you live and what team you're on. You can leave your Pokemon to defend friendly Gyms. When someone else battles and knocks out your Pokemon, it will return with however many Coins it collected, based on how long it defended that Gym, up to a maximum of 50 Coins. Your Pokemon will collect Coins at a rate of 1 Coin per 10 minutes, or 50 Coins after 8 hours and 20 minutes.
Doing a Special Trade every day is useful for re-rolling IVs on your Legendaries, as well as gaining some extra Candy.
Friendship is one of the most powerful mechanics in Pokemon Go if abused correctly. Best Friends gives you a 10% damage increase in Raids, 4 bonus Premier Balls, a 96% Stardust discount on Special Trades, and a chance at becoming Lucky Friends. There are several ways you can raise Friendship:
Battling with a Friend in PvP can yield rewards, up to 3 times a day (You can battle unlimited times, but will only receive 3 rewards a day). 500 Stardust is the most common, but you can also get Rare Candy, TMs, and Sinnoh Stones from PvP. You can also battle with a Team Leader NPC to receive the same rewards once a day.
Once per day, you can encounter a Photobombing Pokemon, usually Smeargle, by using the Go Snapshot feature. The Photobomb will only occur on the first photo of each session - so take one photo, exit, and repeat if you didn't get Photobombed.
This is fairly tedious, but it's 100 extra Stardust a day and can help keep catch streaks alive if you have no spawns nearby.