I've almost optimized everything I can imagine, but being more of a novice there's probably some tricks that I don't yet know of. Here's some pieces of code I believe could be faster, and I'll explain what I've done for each one.

Generation:

Starting Generation:

    // Use this for initialization
    public IEnumerator Generate()
    {

        blocks = new Block[16, 16, 16];

        posx = (int)Position.x;
        posy = (int)Position.y;
        posz = (int)Position.z;


        loadthread = UnityThreadHelper.TaskDistributor.Dispatch(() => blocks = GeneratePlanet.Generate("rock", planet.planetSize, planet.planetSeed, planet.cave, planet.cracked, posx, posy, posz));

        while (loadthread.IsSucceeded == false)
        {
            yield return new WaitForSeconds(0.1f);
        }


        loadthread = UnityThreadHelper.TaskDistributor.Dispatch(() => blocks = GeneratePlanet.GenerateOres(blocks, planet.planetSize, planet.planetSeed, posx, posy, posz));

        while (loadthread.IsSucceeded == false)
        {
            yield return new WaitForSeconds(0.1f);
        }

        Generated = true;
        UpdatePlanetChunk();

    }

- Used threading to increase performance

- Used Coroutines to spread out processing

Actual Generation (Kinda Complicated! ...And the most intensive code):

   public static  Block[,,] Generate(string PlanetType, int planetSize, int seed, bool cave, bool cracked, int posx, int posy, int posz)
    {

        Block[,,] blocks = new Block[16, 16, 16]; 

        int PlanetSize = planetSize;

        int r =  PlanetSize / 2;
        int offsetx = PlanetSize / 2;
        int offsety = PlanetSize / 2;
        int offsetz = PlanetSize / 2;

        for (int x = 0; x < 16; x++)
        {
            for (int y = 0; y < 16; y++)
            {
                for (int z = 0; z < 16; z++)
                {

                    if (blocks[x, y, z] == null)
                    {
                        blocks[x, y, z] = new BlockEmpty();
                    }

                }

            }

        }

        for (int tx = 0; tx < 16; tx++)
        {
            for (int ty = 0; ty < 16; ty++)
            {
                for (int tz = 0; tz < 16; tz++)
                {

                        if (Mathf.Sqrt(Mathf.Pow(tx + (posx * 16) - r, 2) + Mathf.Pow(ty + (posy * 16) - r, 2) + Mathf.Pow(tz + (posz * 16) - r, 2)) <= r - PlanetSize / 2.5)
                        {
                            blocks[tx, ty, tz] = new BlockCore();
                        }

                        else if (Mathf.Sqrt(Mathf.Pow(tx + (posx * 16) - r, 2) + Mathf.Pow(ty + (posy * 16) - r, 2) + Mathf.Pow(tz + (posz * 16) - r, 2)) <= r - PlanetSize / 3.5)
                        {
                            blocks[tx, ty, tz] = new BlockBedrock();
                        }

                        else if (Mathf.Sqrt(Mathf.Pow(tx + (posx * 16) - r, 2) + Mathf.Pow(ty + (posy * 16) - r, 2) + Mathf.Pow(tz + (posz * 16) - r, 2)) <= r - PlanetSize / 5)
                        {
                            blocks[tx, ty, tz] = new BlockSubstone();
                        }

                        else if (Mathf.Sqrt(Mathf.Pow(tx + (posx * 16) - r, 2) + Mathf.Pow(ty + (posy * 16) - r, 2) + Mathf.Pow(tz + (posz * 16) - r, 2)) <= r - PlanetSize / 6)
                        {
                            blocks[tx, ty, tz] = new BlockStone();
                        }


                    }

                }
            }


        



        if (cracked == true)
        {

            var CrackGen = new RidgeNoise(seed)
            {
                Frequency = (float)0.03,
                Lacunarity = 2,
                OctaveCount = 2,

                Exponent = 2,
                Offset = 1,
                Gain = (float)1,

            } * 1;


            for (int x = 0; x < 16; x++)
            {
                for (int y = 0; y < 16; y++)
                {
                    for (int z = 0; z < 16; z++)
                    {



                        float value = CrackGen.GetValue(new Vector3(x + (posx * 16), y + (posy * 16), z + (posz * 16)));

                        if (value > 1.00)
                        {
                            blocks[x, y, z] = new BlockEmpty();
                        }
                    }
                }
            }

        }


        if (cave == true)
        {

            var CaveGen = new BillowNoise(seed);

            CaveGen.Frequency = 0.08f;
            CaveGen.Persistence = 0.4f;

            for (int x = 0; x < 16; x++)
            {
                for (int y = 0; y < 16; y++)
                {
                    for (int z = 0; z < 16; z++)
                    {



                        float value = CaveGen.GetValue(new Vector3(x + (posx * 16), y + (posy * 16), z + (posz * 16)));

                        if (value > 0)
                        {
                            blocks[x, y, z] = new BlockEmpty();
                        }
                    }
                }
            }

        }

        return blocks;


    }


    public static Block[,,] GenerateOres(Block[,,] blocks, int planetSize, int seed, int posx, int posy, int posz)
    {

        var OreGen = new BillowNoise(seed);

        OreGen.Frequency = 0.16f;
        OreGen.Persistence = 0.4f;

        List<Block> OreTypes = new List<Block>();
        OreTypes.Add(new BlockOreUranium());

        foreach (Block ore in OreTypes)
        {


            for (int x = 0; x < 16; x++)
            {
                for (int y = 0; y < 16; y++)
                {
                    for (int z = 0; z < 16; z++)
                    {



                        float value = OreGen.GetValue(new Vector3(x + (posx * 16), y + (posy * 16), z + (posz * 16)));

                        if (value > ore.Rarity() && blocks[x, y, z].BlockName() == ore.BaseBlock())
                        {
                            blocks[x, y, z] = ore;

                        }
                    }
                }
            }
        }

        return blocks;

    }

- Used else-ifs to reduce testing of variables

- Changed to a chunk system to generate one bit at a time

If anyone sees any tips to improve this, thanks!

You need to use a profiler for this. What does your profiler tell you? Where are you actually spending your time? Is this really the bottleneck?

Using threads by itself distributes loads among processors but does not actually reduce the work, typically it causes a slight increase in total work but a division in wall clock time. Distributing your workload can help and is one of the easiest changes to make, but it is also one of the smallest ways to improve code.

After you've used your profiler to determine exactly where the actual bottlenecks are, use Unity's profiler commands Profiler.BeginSample() and Profiler.EndSample() to help isolate exactly where the problems are. Is the problem coming from a large number of calls that can be eliminated? Is it coming from unnecessary processing being done? Is it work that can be done with a different algorithm?

After you've profiled it, and used the profiler to isolate an exact section needing change, make the change and profile some more to make sure it actually improved the situation.

Without reviewing it in a profiler everything about it is guesswork. The change might have an improvement, or it may have no effect at all.

Currently, 82.9% of my lag (during lag spikes) is due to PlanetChunk.Generate() [Coroutine: MoveNext]. I'll try to pinpoint it further and post more, but I am sure it is the generation code.

Shoot. I can only call on the profiler in the main thread.

I agree with Frob, but that said, just looking at it, there are a couple of things that I can guess at:

Your sqrt is unneccessary, you can square both sides of the equation, and you can move the calculation of the various radii your checking against out into variables before the for loops. And then you can give them meaningful names too =) EDIT: If its not clear, I'm referring to (r - PlanetSize / 6)^2, which could be renamed minStoneRadiusSquared.

Also, you'll probably want to invert your for loop order, and do z, y, x, it's more memory friendly. If you are wondering why, imagine if you had a single array that was of length 16*16*16, and think of how you're jumping around in it as you travel through your innermost for loops.

EDIT: Though taking a deeper look, it looks like you're just trying to make blocks of a band of a sphere set type, which seems like something you could make separate iterations, without any radial checks at all, especially since those are going to be constant per planetsize, and your dealing with integers. (Which is why you should really deeply consider frob's questions)

Those ideas actually did increase the speed quite a bit, and cut out some lag spikes.

Found it! Using the profiler in deep profile mode, I figured out my noise being used for cave generation and ore gen was using 6 octaves. Cut it down to one octave, 60fps.