Q:

How to applaud in a teleconference?

Suppose a work culture/environment where, in an in-person meeting, if a presenter does a good job, other attendees express appreciation with applause/clapping.
Suppose now that the same meeting happens with (a) several or (b) all of the participants joining remotely via teleconference, many using headphone + microphone headsets.  If there is a large cohort physically co-located, they can continue with the traditional clapping/applause method.  What is the best way for remote participants to join in a similar expression of appreciation, and is there a good alternative when all participants are remote?  Simple silence doesn't seem to provide the same social function. 

A:

Suppose a work culture/environment where, in an in-person meeting, if a presenter does a good job, other attendees express appreciation with applause/clapping.

and

What is the best way for remote participants to join in a similar expression of appreciation, and is there a good alternative when all participants are remote?

As you said, when it is in-person things are different. In such context an applause will make sense and have a meaning. 
When remote things are different. Usually there is no room for applause for several reasons, most of them practical. 
Several people clapping to their microphone will surely saturate the audio of the call, not to mention that it will not have the impact an in-person applause has (clapping alone in your desk looking at a screen is also an interesting image). 
If you feel like thanking or express appreciation to someone and you are remote, you could consider writing some words on the call chat. You could also consider just saying "Thanks a lot, good job" to your microphone when the presentation ends. 
In a way, this also depends on your company culture and practices regarding remote presentations, and at the end of the day you should go for what is best for you and your context. Perhaps you already have some handbook/practices regarding remote conferences.

