To me 'What's that' is somewhat more polite than 'Come again?', and both are somewhat more polite than just 'What?' or especially 'Huh?' But all of those leave something to be desired in a public setting such as a conference. Actually, for my taste, anything longer is better in any setting, e.g.,
I beg your pardon?
Sorry, could you repeat that?
Could you say that again, please?
I sometimes have the feeling that people who are hard of hearing slip into the habit of using the shortest form possible, whether it's polite or not. I don't know if they think we get tired of hearing the longer forms, or whether they just get tired of saying them and frustrated at having to ask people to repeat themselves. (My dad, for example, seems convinced that it's a conspiracy of everyone else to speak softer. (-; ) But it can certainly also get frustrating for the hearers.
To me it would be better to address the problem once at greater length, e.g.: 'I'm afraid I'm having trouble catching what several of you are saying. Could I ask you all to speak up a good deal more?' Especially at a conference, where international accents might exacerbate the problem, that could be helpful. It might even spur someone to produce a second microphone for the questioners, or to station a relay person halfway to repeat questions as necessary.