Just tell them...my husband and I both agree that we'd much rather the other person tell us about something unpleasant rather than discover later that we've been subjecting others to it all along. For instance, if he's been working all day and we're getting ready to go somewhere, he knows that "Were you going to take a shower before we go?" translates into "You stink, you might want to do something about it." It's not always easy to bring it up, but it will be appreciated later. Anyone who loves you and knows you love them should be able to accept that you have their best interests in mind and you're not saying it to hurt their feelings or make them self-conscious.
In the case of bad breath, if the person brushes regularly already then it's a matter of concern for their dental health. Let them know that you're worried there might be something wrong and suggest a visit to the dentist to find out if there's an underlying cause. My ex developed bad breath at one point in our relationship, and at first I ignored it...but it got worse every time he brushed. Though he was initially offended that I brought it up, he went to the dentist and discovered that he had an advanced cavity, and every time he brushed it cleared out the gunk enough for me to smell it rotting. He was grateful to know about it, and because I mentioned the smell (repeatedly) he got to the dentist before it would have required a root canal.