You see these a lot with business acquisitions: the seller pretty much has no choice but to disclose all sorts of things, but they want protection if the deal falls through.
You'll also see these in connection with employment contracts. Or 3rd-party service agreements (e.g., the development of custom software). Joint ventures, too.
Confidentiality agreements are sometimes included in other agreements (e.g., a letter of intent). They can be separate, though, and there are reasons to go either way.
You'd think confidentiality agreements would be a big deal between startups and VCs. But apparently that's not how it usually proceeds: VCs won't sign these (all they do is go around looking for businesses to invest in-- they've probably got eyes on several similar startups at any one time, and they don't want to be accused by paranoid folks they didn't fund). So don't ask them to: it just makes you look clueless.
How do you protect against claims like that? Some companies (who have been burned in the past) simply refuse to consider unsolicited ideas at all: they just return them to the sender. That might be an overreaction.
But you can create a system whereby you can look at unsolicited ideas without incurring too much risk. First, have them screened (i.e., processed in the mailroom) by a non-technical person who wouldn't know if it has any commercial viability, but can identify it as an unsolicited submission. Then immediately send a letter denying any confidentiality obligation or arrangement, but include a release and waiver form, which (if it gets signed) will let us examine your work.