Which tools do you use to analyze waveform data from simulation or logic analyzer traces?
For the use cases you describe, I typically write python scripts to do the job.  There are good plotting facilities available in python (matplotlib et al) and it's often faster to write your own script if you're looking for something specific.  I don't have experience with the Xilinx tools, but if they can export the data to a format that's easy to parse, it's not a bad option.