There's a similar question which covers some of this: Security risks of rooting your android smartphone. However, since it doesn't really explain how you manage access to the root user, I'll expand on that here.
When you root your device, you basically always (technically I suppose you don't have to, but you should) install the Superuser application along with the
su binary. Superuser's sole purpose is to manage which applications are permitted to elevate to root and which are not. The default behavior is that Superuser will prompt you whenever a new app tries to execute a call to
su, and you can then allow or deny it using the prompt. It can save your decisions so that you won't get prompted more than once for the same app, but you can erase this saved data from the Superuser settings page. It also provides a log viewer which keeps track of when
su is accessed and by which applications.
Now, the tricky part is that many of the newer malicious apps will actually perform an exploit to gain root access rather than simply trying to make a call to
su. There's really not much you can do about these aside from being careful about what you install and where you install apps from since they aren't even using
su to begin with. However - to directly answer your question - apps which require legitimate root access can be easily managed by Superuser as explained above.
If you are rooted but don't already have Superuser then you should be able to simply install it from the Market, I believe.