According to the wikipedia article on memory segmentation, x86 processors do segmentation bounds-checking in hardware. Are there any systems that do the bounds-checking in software? If so, what kind of overhead does that incur? In the hardware implementations, is there any way to skip the bounds checking to avoid the penalty (if there is a penalty)?
All modern languages do bounds checking in software, on top of segment bounds checking and memory map lookups. One benchmark suggests the overhead is about 0.5%. This is a small price to pay for stability and security.
A 486 could load a memory location in a single cycle, and CPUs have only gotten better at doing on-chip processing, so it's unlikely that segmentation bounds checking has any overhead at all.
Still, though, you can simply run in 64bit mode: "The processor does not perform segment limit checks at runtime in 64-bit mode" (Intel's developer manual, 3.2.4).