My impression to this point had been that it wasn't specific to geeks but rather to speakers who are a bit uncomfortable. For example, I recall hearing a lot of students use it all the time while nervously giving presentations, desperately trying not to de-rail their trains of thought.
As geeks tend to be more socially awkward, I'm fairly certain it actually has less to do with geekiness and more with lack of confidence -- I've seen decidedly non-geeks do it when they're nervous.
As for the "So, ..." with a pause for dramatic effect:
I find that the implications tend to depend on context. I can confirm the use with the meaning of "I will try to explain concepts unfamiliar to you using analogues hopefully more familiar to you and this is going to take me some mental effort" but I disagree that this is specific to geeks, unless you define "geek" as "someone more familiar with a given topic than you".
I can also confirm its use followed by a summary of what the other person said ("So, ... you're saying this is a bad idea?").
I don't think the use to re-boot a conversation after an awkward pause or to change the topic is as common in German, though other fillers like "Okay, ..." tend to be used the same way.
The functions definitely aren't unique to English and there is a lot of overlap in the words being used. The author comes off as a bit too much of an armchair linguist for my taste.
http://en.wikipedia.org/wiki/Filler_%28linguistics%29#Filler...