The fugue in the Chromatic Fantasy and Fugue is not "mostly one voice in a straight line"! It's densely contrapuntal and is viciously hard, if not nearly impossible to play at a keyboard speed with proper legato. It, most of the keyboard Partitas, and the Goldberg Variations are probably the hardest overall.
Sorry, I should have been clearer: I was referring to the Fantasia, not the Fugue. The Fugue is also crazy hard!
In general, I'd say that dense counterpoint is the biggest challenge in playing Bach on guitar. That's why I would say a fugue of some sort (whether it be 903, 997, 998, 1000, etc.) is probably the top spot in my book. I just don't know them well enough. I'm terrified of the idea of having to concertize one!