How to interface OV5640 to Arduino Mega using Embedded C?
Arducam gives you all the info you need on the necessary register settings. The register values for each color space and resolution are defined in this header while the initialization sequence, image format selection and image capture process among other stuff, are implemented here and documented if you look closely at the variable names and compiler directives. 

EDIT: More details

Lines 327 - 372 contain the relevant initialization sequence for this specific camera. For instance, assuming you want JPG images, line 335 marks the start of the needed settings:

delay(100);
wrSensorReg16_8(0x3103, 0x11);
wrSensorReg16_8(0x3008, 0x82); delay(100);
wrSensorRegs16_8(OV5640YUV_Sensor_Dvp_Init); delay(500);
wrSensorRegs16_8(OV5640_JPEG_QSXGA);
wrSensorRegs16_8(OV5640_QSXGA2QVGA);
wrSensorReg16_8(0x4407, 0x0C);  # assuming you arent using the Arducam shield or OV5640 5MP Plus


What wrSensorReg16_8 does is pretty obvious: write the 8-bit 2nd argument into the register specified in the 16-bit 1st argument. wrSensorRegs16_8 merely does the same thing for multiple register-value pairs passed into it. OV5640YUV_Sensor_Dvp_Init, OV5640_JPEG_QSXGA and OV5640_QSXGA2QVGA are all structs defined in the header I mentioned earlier; they contain the rest of the register-value pairs you need to know about. Ultimately, these settings should give you 320x240 JPEG, I think. 

You can't use the start_capture method since you don't have the ArduCAM FIFO so you'll have to start grabbing frames yourself (and buffering them somewhere very quickly; transmitting the bytes as you read them is out of the question) by paying attention to VSYNC, HREF and PCLK. Look at the timing diagrams in the datasheet. I assume you'll only be taking frames occasionally since a Mega won't do for video. If you're very lucky, you'll get a nice image on your first try but on the whole, be ready to spend serious time studying the datasheet, ArduCAM code and other 0V5640-related code on the web or just go with the OV7670 which has more examples/tutorials.