Resource Gathering Hints

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Scouting

Keep a log of the systems you've visited. Note those with resource-rich planets that are too hostile to land on. You may be able to come back to them later.
Notice how the orbits of planets are different colors? Figure out what they mean and it can save you some time.
Many planets have satellites which you can land on. Most of these are Gas Giants, such as the planet Jupiter, and you can't land on them, but don't assume all planets with satellites are Gas Giants. Some aren't, and you can land on them as well as their satellites.
You should also note that different star systems have different temperatures. Generally, the higher the temperature, the bigger the mineral batches will be. Go for hot - but not too hot as it may prove risky. Note that giants or SuperGiants may prove to be too hot to access.

Collecting

Talk to the starbase commander about resource gathering.
Don't waste time and fuel on gathering common or corrosive metals. They don't give you very many RUs.
Collect biological data even if you don't know what to do with it yet. It's pretty safe to say it's there for a reason.
Fuel is expensive. It's more efficient to completely clear a system than to go back twice. If you run out of room and there's still good stuff in the system, consider dumping some of your cheapest cargo.
Make sure mineral quality and quantity is worth the fuel cost, especially for planets with high gravity. When you click to dispatch a collecting ship, note that the fuel that the trip will consume is displayed above its little picture. You can opt out of making the trip by hitting the usual cancelling button. Over the course of this game, you will find many planets that only have a few tiny spots of Type 1 resources and ought to leave them unharvested.
Fuel is valuable. If you find aliens who trade for it you can sell it back at the starbase for huge returns in RU's. This is the equivalent of collecting expensive minerals.

Random Hostile Encounters

The Ilwrath Avenger will prove to be a very risky fight, one slip and you face serious damage.
Always be prepared to fight a Slylandro Probe. You can pick every battle except this one.
Get really good at killing Ilwrath and Slylandro. Practice against them in Super Melee.
Around a star, alien ships often move about at random from planet to planet. Sometimes you can sneak in to take resources from a planet that an enemy ship has just left.
You can gather resource units easily if you encounter a race which is a poor match for your ships. There is a near-infinite supply of enemy ships in a star system and you can gain a considerable amount of resource units by scavanging their debris. Combat salvage does not require a Storage Bay, so the length of a hunt is limited only by your combat skill and crew complement.

Reconfiguring the Flagship

You lose no money selling ships and modules; it's cost-effective to rework your flagship and fleet to suit whatever task you're planning. If aliens give you ships you don't fly well, sell them.
Always keep a couple of fleet combat ship positions open when visiting alien species so you can receive ships as gifts.
If you're mining bring extra landers and as many storage bays as you can afford. Also remember to bring around 15 extra units of fuel per Storage Bay — every landing costs fuel. Lastly, pack an extra crew pod. Planet landings are hazardous.
Remember that a lander costs 500 RU, and that when you lose one, you also lose the cargo on board.
Depending on what you're hunting, the best "Bounty Hunter" configuration might be an unarmed mothership with extra crew pods supporting a fleet of combat ships particularly suited to your chosen prey.
Some regions are safe from space combat, so you can optimize your flagship for massive resource collection to clean these out, rather than wasting fuel on several trips with a flagship configured for battle just in case.

Improving the Flagship

Early on in the game, technological advances may prove more useful than knowledge about your enemies by improving your resource-gathering and combat capabilities. Try to find a race willing to trade technologies or items with you.
Invest in thrusters. They affect your flagship in all areas of the game, and can get you from system to system (and away from enemies!) much faster. The number of thrusters does not affect fuel consumption.
Turning jets are not as important as thrusters, but they make navigating and avoiding enemies easier. They also save you valuable game time while reorienting your ship in HyperSpace.

Interstellar Navigation

Remember that time passes very quickly outside a solar system. Know where you want to go and use the autopilot to get there.