I worked with a guy many years ago who coined the term "worthy bugs" that we used when we had a really good one. Two, in particular, I remember decades later.
1. This turned out to be a hardware bug that showed up in our software very intermittently. In the 1980's, National Semiconductor offered the NSC 880, a clone of the 8080: Same instruction set, mostly the same specs. This processor is spec'ed such that on the enable interrupts instruction, interrupts are not actually enabled for one instruction cycle so as to allow for a bit of cleanup (pop or whatever) without interruption. Without this, stacks could become confused, and did. Well, the guys at the fab across the street from where we were doing software development did not implement this one-instruction delay, but kept knowledge of it as a secret errata. When confronted about it after we had traces that proved the error in hardware, their response was "well, we didn't think it would ever come up." Bastards.
2. It turned out that one of the early Intel chipsets implementing PCI would, when doing 64K data transfers that fell exactly on 64K boundaries, deliver the first byte of the the range in place of the last byte. I was working on Ethernet device drivers at the time, so this just looked like data corruption in the driver or the network controller to us. It took a while and many logic analyzer traces to root cause this one to the chip set. Once we knew what was happening, the software work-around was easy, but it did slow down the driver just a bit. At least the chip set guys were unaware of this bug, and it never appeared in the many subsequent chip set implementations of PCI.