You can put as many circuits as you want in the conduit (subject to the conduit fill rules). Do note that if you run more than three current carrying wires in the conduit you will have to derate which may mean increasing the wire size. If you run two independent circuits, that would be FOUR current carrying wires.

You can use whatever colors you want to keep things straight as long as your hots are some other color other than green or white. More often than not everything is black.

Running THHN through the conduit allows you to derate and still make 20A.
Another out is to ditch the GFCI receptacles for a GFCI breaker and install a multiwire branch circuit (which would be allowed to share the neutral providing for only 3 current carrying conductors).

Your biggest issue is 1/2" PVC is going to be too small. It's legal limit is 4 #12's. You'll not get two independent circuits in there (that would take 5 wires at least). The other thing to watch out is for your box fills, you need to count the conductors that pass through even if they don't terminate at a device or are otherwise spliced there.

As for the lights and the garage doors, again you can run wires together again as long as you don't exceed the conduit fill rules and wire ampacity rules.

Again the same applies for your 240V circuits (other than the fact you can't have a MWBC for 240). The code only mandates garages (at or below grade) to have GFCI's for the 120V 15 or 20A receptacles. It is up to you to decide if you want or need GFCI protection on the 240 circuits. They most certainly do make 240V GFCI breakers. They're a bit pricy and the borgs do carry them for some of the more popular panel brands. Otherwise, unless you can wrangle the trade discount out of the local electrical supplier, you can find them on the Internet at competitive prices.

The ground wire doesn't need to be insulated or in conduit except as necessary to be protected from physical damage. I might sleeve it where it emerges from the ground for a 18" or so. It's not a strict code requirement, but frankly if direct buried stuff can be damaged emerging from grade, so can your ground. Keep it safe from weed whackers and other careless gardening.

The fact that you put ground rods in seems to imply this is a separate structure. Did you run both a neutral and ground with your feeder?

Time available does not permit posting my suggestions to all your questions. But one suggestion is to keep every electrical box at least 18" above the floor level. Lower installations may require the use of materials suitable for Class 1 locations.

The feeder is two hot, neutral, ground. Neutral bar in subpanel is not bonded.

Arrgh about the 1/2'' conduit being too small. I fear I'll end up running each circuit in it's own conduit system, then. (I thought 1/2'' was logical as the female holes in the outlet and switch boxes were 1/2''.)

I am keeping all outlets at 50'' height, as I want them to be above work counters and tools.

You can run up to eight 12ga THHN wires in 1/2" conduit, so your plan for running two circuits is fine. If you run two independent circuits you need two hots, two neutrals, and one ground (can serve both circuits). You will need to to make sure the neutrals are kept separate for each circuit.

Depends on whether you are using sched 40 or sched 80 conduit. I inadvertently gave the numbers for sched 80.

I'm using sched 40, sorry - I should have stated that.

I had sched 80 on the brain because you can't use sched 40 for protection from physical damage.