If a college application asks me what the best invention was would it be bad to say birth control?

so long as you can argue it well, it could work. i would suggest going with penicillin or maybe the wheel

Yes.
Doesn't matter what you think, if you speak about racial, religious, or sexual differences it will ALWAYS get misunderstood, lol.

I think birth control is tough topic to defend and is a touchy issue. It can show that you're willing to stand up for your ideas despite the possibility of them being challenged. I personally plan on having no children, so yes, great invention. It gives women the power to choose for themselves when and if they'll have children, lowers the population, etc. But keep in mind, committee members may hold strong religious reasons for disagreeing with you. Good luck.

In relative terms, there are a few colleges that might be impressed, but on an average you are more likely to see more negative than positive in relative terms. There are many people not interested particularly in women's freedom, and further abstinance did not need inventing. Also, there are negative implications of the forced sterilization that has and still does occur. Birth control is not even technically an invention unless referring to a specific device and arguing its benefit versus other types.  I don't think "bad" is the right word, but relatively weak choice would be accurate.
There are many things that are more positive.
Antibiotics (such as penicillin), computers, telephones, or other things on this nice list:
http://www.i-dineout.com/pages2003/inventions1.html
For a college application, you can choose something interesting. For example, a wheelchair is the greatest invention if all time. Invented in the 1590's, it allows many handicapped people to be productive members of society. You can add in a personal experience in a few lines and cite any number of people in wheelchairs who have made great contributions such as Stephen Hawking, who without the wheelchair, might never have been able to learn and contribute.
You can choose almost anything, but the idea of a college application is to show how important something is to all of society and hopefully be able to personalize the essay(or answer) a little.
If you got a Mormon or Conservative Christian reading your application, it would certainly not read very well.
Adding: How about a water filter? It is used to save millions of lives and is an essence of what keeps us alive. If placing a birth control device against a water filter, it is easy to put things in perspective.