Another useful tool, if one does SPI/I2C bus debugging a lot and can afford it, is a tool like the Aardvark, whose software is designed around bus debugging. In particular, compared to a pure logic analyzer, you can also write things to the bus as needed. But there are many, many ways to skin this cat, including DIY solutions like the Nucleo board dieter1 mentions (or any other fast MCU with enough buses for your situation).