2. Research Labs. What is a good number of labs to have running? I'm not sure what would be considered too little or too much when I add research labs to my space ports.
Standard empires want their total lab capacity to at least equal their empire research potential. You can see the empire's research potential and the total capacity in each field in the rightmost tab of the research screen; determining whether you've met the goal of matching total capacity to empire potential can be done by summing the total capacities across all fields and comparing the result to the empire potential.
Pirate empires are a bit different; they essentially perform no research until they transition to be planetary empires, but after that point they can have enormous research potentials due to the bonus to research potential offered by the special pirate facilities. The research potential of planetary pirate empires can be so great that it is impractical and unnecessary to match the empire's total lab capacity to its research potential, and so for pirate empires it can basically boil down to how much you're willing to invest and what research rate will satisfy you.
6.
I have not found a way to improve the quality of low quality planets. I cannot even find any tech to research that might help in this regard.
Perhaps add this to the wishlist?
That would be because there is no such technology. The only terraforming structure available speeds the rate at which damaged planets recover their original quality but does not improve planet quality over time. There are a couple of events that can affect planet quality, though most of these temporarily reduce planet quality rather than permanently improving it (there are nevertheless occasional events which slightly improve a planet's quality).
The only way for the player to actively alter a planet's quality without resorting to the game editor is bombardment, which with standard weapons can only reduce planet quality (and that only temporarily, and only if the planet lacks a planetary shield generator). Permanent reductions in planet quality can be obtained by use of a superweapon (although I'd class this less as a 'reduction' of planet quality and more as the destruction of the planet).
4. Mine EVERYTHING. When I expand, I pretty much try to mine every resource in ever system no matter how small the percentage is. Is this a problem? Should I build star bases or spaceports in this systems?
I would not mine anything approaching 'everything,' except perhaps in the very early stages of the game. I prefer to only mine targets which offer multiple resources, preferably summing to 100% or more resource quality (e.g. 50% steel + 50% gold), and furthermore prefer mining targets relatively close to colonies and places where I want to put shipyard capacity (which gets built over colonies; my experience is that freighters do not do a great job keeping shipyards which are not over colonies supplied with resources). Fuel sources are the only exception to this, and I'll still ignore poor sources of fuel if my fuel options in the region are adequate without them.
You just don't need the resource production found in mining everything; you're going to have downtime in ship construction and colonization which allows your existing mines to start building up a stockpile as the game goes on, and it's only really in the early stages of the game that you're all that likely to run into more than localized resource shortages. Beyond that, especially if you like heavily fortified mines, mining everything can be a real drain on your private sector's money, limiting its ability to purchase, maintain, and fuel the freighters needed to move those resources around. Having a few mines on decent sources for each strategic resource near each shipyard is generally sufficient, though you can almost always use more fuel.
3. What do you do with planets without resources? All I ever do is put either resort or research labs on them...what does everyone else do?
Is it a reasonable colony prospect despite its lack of resources (quality over ~60% and preferably much higher, large size, extends my colonization range if I'm playing with colonization range limits enabled, extends my claim region over something that I'd like to claim somewhere down the line such as a good quality planet I can't colonize yet or a superluxury or rare strategic resource that I'd like to claim or prevent another empire from mining, etc)? If yes, then put a colony there. Have I reached a point in the game where I don't really have more worthwhile colonization targets? Reevaluate the colony to see if it's worth bothering with on the basis of its quality and size (i.e. future income potential).
Does it offer a scenery bonus and is it relatively close to existing (preferably large) colonies? If yes, then a resort wouldn't be a bad idea. Does it offer a research bonus superior to anything else I have? If yes, a research base with the appropriate labs would not be a bad idea. Even if the research bonus doesn't exceed what I already have, it might be okay to build a lab there either to deny another empire access to it or to boost my research capacity to meet empire potential (though if meeting empire potential is the only goal, I tend to prefer somewhere safer, such as over a colony with a big spaceport).
If it doesn't meet any of the above criteria, I wouldn't bother with it. If there are better options available for extending colonization range or staking a claim to a useful location, I wouldn't immediately bother with it and maybe won't bother with it at all.