A Very Bad Idea is just that: a very bad idea.
It very nearly always guarantees that something bad will happen if it is actually gone through with. These somethings tend to be self-injury, injury of others, death, explosions, general destruction, and possibly some very angry people if they were close enough to the bad results.
Understandably, Very Bad Ideas are very popular at HQ among agents who are more insane than the average agent. Many of them may be found on the list of Things I Am Not Allowed to Do at the PPC.