I'm dubious that there's any scientific knowledge that it's intrinsically unethical to have* -- things we're "not meant to know." But it is clear that there are some things that it's unethical to find out, because ethics bars us from using some methodologies. Pretty much everyone recognizes this -- you'd have a hard time finding anyone who thought the Tuskegee syphillis study was justified, or who is disappointed that B.F. Skinner didn't really raise his daughter in a box to see what would happen. If there were some piece of knowledge that we could only get from a study like one of those, I think we'd all agree that the world will just have to do without that knowledge.
It's frustrating, then, to see the way many defenders of science seem to fall into the mad scientist storyline when discussing other proposed ethical restrictions on scientific research, such as repatriation of Native American remains, bans on animal research, or bans on stem cell research.
The issue is not whether you agree with the claims -- I happen to think the above-mentioned proposals are justified, sometimes justified, and unjustified, respectively. The issue is whether you recognize them as ethical concerns and respond to them on their own terms. It's fine to argue either that the claimed ethical concern is groundless (e.g. because being a morally considerable being depends on X criteria, which embryos or animals don't have), or that it's outweighed by the intrinsic and/or instrumental value of the resulting knowledge (e.g. all of the examples I've used have been claimed to produce knowledge useful for curing deadly diseases, so an argument could be made that a certain level of killing or stealing is a justified -- or even obligatory -- cost). What raises the specter of the mad scientist is to respond with outrage that someone would dare question science, and to present the advance of scientific knowledge as a self-evident moral imperative that trumps everything else. "There's no other way to find out X" is only a complete justification for research to a mad scientist -- sane scientists have to go on to argue that the ethical pros and cons of the research are of certain magnitudes and the former outweighs the latter. (And sane opponents must do likewise, or at least make an argument that the harms in question trump any other concerns**.)
On the other hand, it doesn't help when those proposing the restrictions oversell the possibility of having your cake and eating it too. Native American traditional knowledge, tissue cultures and computer simulations, and adult stem cells are all worthy avenues of research to have available if we decide that the associated restriction on other methodologies is justified. But none is a complete replacement, and so the critics would do well to face up to the fact that their ethical concerns will result in the world foregoing some knowledge.
*As opposed to particular facts, such as information about someone else's personal life, which there can be ethical problems with knowing.
**It's far more plausible (especially if you hold a strong version of the act-omission distinction) to think that killing always trumps the advance of knowledge than the other way around.