These are backups of functions that are apart of GT/GameTools. I do not at all claim that they are well written, but they do the trick for me so far.

Edit: Nov 17 2016 - Fixed a bug in DXT3 alpha being byte swapped.

public static Color[][] ReadDXT1(GTFS fs, bool flip, int width, int height) {
	int total = width * height;
	Color[][] blocks = new Color[total / 16][];
 
	for (int i = 0; i < total / 16; i++) {
 
		byte[] raw = GT.ReadBytes(fs, 4, flip);
 
		ushort c0, c1;
		if (flip) {
			c0 = (ushort)(raw[2] | raw[3] << 8);
			c1 = (ushort)(raw[0] | raw[1] << 8);
		} else {
			c0 = (ushort)(raw[0] | raw[1] << 8);
			c1 = (ushort)(raw[2] | raw[3] << 8);
		}
 
		// Color 0 RGB
		byte r0 = (byte)((c0 >> 11) << 3 | 0x04);
		byte g0 = (byte)((c0 & 0x07E0) >> 3 | 0x02);
		byte b0 = (byte)((c0 & 0x001F) << 3 | 0x04);
		// Color 1 RBG
		byte r1 = (byte)((c1 >> 11) << 3);
		byte g1 = (byte)((c1 & 0x07E0) >> 3);
		byte b1 = (byte)((c1 & 0x001F) << 3);
		//--
 
		Color[] cx = new Color[] {
			Color.FromArgb(Byte.MaxValue, r0, g0, b0),
			Color.FromArgb(Byte.MaxValue, r1, g1, b1),
			(c0 > c1) ? Color.FromArgb(byte.MaxValue, (2 * r0 + r1) / 3, (2 * g0 + g1) / 3, (2 * b0 + b1) / 3) : Color.FromArgb(byte.MaxValue, (2 * r1 + r0) / 3, (2 * g1 + g0) / 3, (2 * b1 + b0) / 3),
			(c0 <= c1) ? Color.FromArgb(byte.MaxValue, (2 * r0 + r1) / 3, (2 * g0 + g1) / 3, (2 * b0 + b1) / 3) : Color.FromArgb(byte.MaxValue, (2 * r1 + r0) / 3, (2 * g1 + g0) / 3, (2 * b1 + b0) / 3)
		};
 
		uint pixels = GT.ReadUInt32(fs, 4, flip);
 
		int p15 = (int)((pixels & 0xC0000000) >> 30);
		int p14 = (int)((pixels & 0x30000000) >> 28);
		int p13 = (int)((pixels & 0xC000000) >> 26);
		int p12 = (int)((pixels & 0x3000000) >> 24);
		int p11 = (int)((pixels & 0xC00000) >> 22);
		int p10 = (int)((pixels & 0x300000) >> 20);
		int p9 = (int)((pixels & 0xC0000) >> 18);
		int p8 = (int)((pixels & 0x30000) >> 16);
		int p7 = (int)((pixels & 0xC000) >> 14);
		int p6 = (int)((pixels & 0x3000) >> 12);
		int p5 = (int)((pixels & 0xC00) >> 10);
		int p4 = (int)((pixels & 0x300) >> 8);
		int p3 = (int)((pixels & 0xC0) >> 6);
		int p2 = (int)((pixels & 0x30) >> 4);
		int p1 = (int)((pixels & 0xC) >> 2);
		int p0 = (int)((pixels & 0x3));
 
		if (flip) {
			blocks[i] = new Color[] {
				cx[p15], cx[p14], cx[p13], cx[p12],
				cx[p11], cx[p10], cx[p9], cx[p8],
				cx[p7], cx[p6], cx[p5], cx[p4],
				cx[p3], cx[p2], cx[p1], cx[p0]
			};
		} else {
			blocks[i] = new Color[] { cx[p0], cx[p1], cx[p2], cx[p3],
				cx[p4], cx[p5], cx[p6], cx[p7],
				cx[p8], cx[p9], cx[p10], cx[p11],
				cx[p12], cx[p13], cx[p14], cx[p15]
			};
		}
	}
 
	return blocks;
}

public static Color[][] ReadDXT3(GTFS fs, bool flip, int width, int height) {
	int total = width * height;
	Color[][] blocks = new Color[total / 16][];
 
	for (int i = 0; i < total / 16; i++) {
		byte[] rawalpha = GT.ReadBytes(fs, 8, flip); //Each pixel gets 4 bits for alpha
 
		byte[] raw = GT.ReadBytes(fs, 4, flip);
 
		int[] alpha = new int[rawalpha.Length * 2];
 
		for (int a = 0; a < rawalpha.Length; a++) {
			alpha[a * 2] = (rawalpha[a] & 0x0F) * 17;
			alpha[a * 2 + 1] = ((rawalpha[a] & 0xF0) >> 4) * 17;
		}
 
		//http://www.igeekstudio.com/blog/dtx1-decompression-explained
		ushort c0 = (ushort)(raw[0] | raw[1] << 8);
		ushort c1 = (ushort)(raw[2] | raw[3] << 8);
 
		// Color 0 RGB
		byte r0 = (byte)((c0 >> 11) << 3 | 0x04);
		byte g0 = (byte)((c0 & 0x07E0) >> 3 | 0x02);
		byte b0 = (byte)((c0 & 0x001F) << 3 | 0x04);
		// Color 1 RBG
		byte r1 = (byte)((c1 >> 11) << 3);
		byte g1 = (byte)((c1 & 0x07E0) >> 3);
		byte b1 = (byte)((c1 & 0x001F) << 3);
		//--
 
		Color[] cx = new Color[] {
			Color.FromArgb(Byte.MaxValue, r0, g0, b0),
			Color.FromArgb(Byte.MaxValue, r1, g1, b1),
			(c0 > c1) ? Color.FromArgb(byte.MaxValue, (2 * r0 + r1) / 3, (2 * g0 + g1) / 3, (2 * b0 + b1) / 3) : Color.FromArgb(byte.MaxValue, (2 * r1 + r0) / 3, (2 * g1 + g0) / 3, (2 * b1 + b0) / 3),
			(c0 <= c1) ? Color.FromArgb(byte.MaxValue, (2 * r0 + r1) / 3, (2 * g0 + g1) / 3, (2 * b0 + b1) / 3) : Color.FromArgb(byte.MaxValue, (2 * r1 + r0) / 3, (2 * g1 + g0) / 3, (2 * b1 + b0) / 3)
		};
 
		uint pixels = GT.ReadUInt32(fs, 4, flip);
 
		int p15 = (int)((pixels & 0xC0000000) >> 30);
		int p14 = (int)((pixels & 0x30000000) >> 28);
		int p13 = (int)((pixels & 0xC000000) >> 26);
		int p12 = (int)((pixels & 0x3000000) >> 24);
		int p11 = (int)((pixels & 0xC00000) >> 22);
		int p10 = (int)((pixels & 0x300000) >> 20);
		int p9 = (int)((pixels & 0xC0000) >> 18);
		int p8 = (int)((pixels & 0x30000) >> 16);
		int p7 = (int)((pixels & 0xC000) >> 14);
		int p6 = (int)((pixels & 0x3000) >> 12);
		int p5 = (int)((pixels & 0xC00) >> 10);
		int p4 = (int)((pixels & 0x300) >> 8);
		int p3 = (int)((pixels & 0xC0) >> 6);
		int p2 = (int)((pixels & 0x30) >> 4);
		int p1 = (int)((pixels & 0xC) >> 2);
		int p0 = (int)((pixels & 0x3));
 
		blocks[i] = new Color[] { cx[p0], cx[p1], cx[p2], cx[p3],
				cx[p4], cx[p5], cx[p6], cx[p7],
				cx[p8], cx[p9], cx[p10], cx[p11],
				cx[p12], cx[p13], cx[p14], cx[p15] };
 
		for (int k = 0; k < blocks[i].Length; k++)
			blocks[i][k] = Color.FromArgb(alpha[k], blocks[i][k]);
	}
 
	return blocks;
}

Thanks to Asger Hoedt

private static int MortonSeparateBy1(int x) {
	x &= 0x0000ffff;
	x = (x ^ (x << 8)) & 0x00ff00ff;
	x = (x ^ (x << 4)) & 0x0f0f0f0f;
	x = (x ^ (x << 2)) & 0x33333333;
	x = (x ^ (x << 1)) & 0x55555555;
	return x;
}
 
public static int Morton2D(int y, int x) {
	return MortonSeparateBy1(x) | (MortonSeparateBy1(y) << 1);
}

public static Color[][] ReadCMPR(GTFS fs, bool flip, int width, int height) {
	int total = width * height;
	Color[][] blocks = ReadDXT1(fs, flip, width, height);
 
	//The blocks require reordering...
	int rows = height / 2;
	int cols = width / 2;
	Color[][] reorder = new Color[total / 16][];
	int i = 0;
	for (int y = 0; y < rows; y += 4) {
		for (int x = 0; x < cols; x += 4) {
			reorder[i++] = blocks[y * rows / 4 + x + 0];
			reorder[i++] = blocks[y * rows / 4 + x + 1];
		}
		for (int x = 0; x < cols; x += 4) {
			reorder[i++] = blocks[y * rows / 4 + x + 2];
			reorder[i++] = blocks[y * rows / 4 + x + 3];
		}
	}
 
	for(int z = i; z < blocks.Length; z++) {
		reorder[i++] = blocks[0];
	}
 
	return reorder;
}