Answering e-mails with just 'Thank you' Lately I have been applying to many universities for a position on a master's program, therefore I contaced many people asking them questions regardings these programs. What troubles me is the following:

When I recieve an answer, am I supposed to answer saying "Thank you" or something like that? 

My reasoning is that these people (secretaries and such) have too much work and having an email at their inbox just thanking them will just cause iriation and disorganization.
This can depend on a lot of things, but mostly on how much the other person did to help you and how much it would be part of their normal job. But in some situations, a simple thank you, totally appropriate in person, is, as you say, just noise that takes effort to deal with. 

I often don't send such thank you emails myself, for this reason, and wonder, as you do, if I'm doing the right thing. And I find thanks you notes back to me as just an additional task to handle. 

I sometimes add "thanks in advance" to the end of a simple response, getting it out of the way. Sometimes the return thanks is just assumed by the receiver, in any case. 

But I don't think that "in person etiquette" is really identical to "online etiquette" and that we have to wait for some time to pass until everyone is comfortable with the difference. In the short term, use your judgement. 

But, after a sequence of questions and responses, it is probably more important to give thanks at the end. And if you don't send individual "thanks" but later meet the person, you can then say "thanks for your help in the past".