Question: I find myself using these words *all the time*. 

Now (<-- there's one!), to be clear the context I'm using them is in conversational style writing, on social commentary, or in forum posts like these. It's not formal academic writing, and it's not story telling. (In a fictional story, these words would be perfectly appropriate if used by a character). 

Here's an example where I've used it recently:

> 
> Point four, I think it is realistic that people would have this interpretation. **So** on this point I'll just stress that this blog post is not intended to be malicious or make anyone feel bad. It's more an interesting exploration of social interaction and how best react and navigate it. 
> 
> 
> 

My question is - is this actually an effective writing style, in the sense of being easy to read and persuasive, and if not, how do I get around it?

Answer: 
In your example, the word may soften up the sentence and paragraph, but it remains spoken English, and does give the impression you're not entirely sure of what you're saying. Consider the following:

> 
> So on this point I'll just stress that (...)
> 
> 
> 

vs.

> 
> On this point I'll just stress that (..)
> 
> 
> 

In this particular case you can afford to simply remove the word; the sentence becomes more affirmative. 

These words are usually markers of hesitation. They're slightly less noticeable when you speak, but in written form you should try to avoid them, especially if you're trying to make a point.
Filler words can help you reach a higher word count, but if you want to be more concise, delete them. I find that filler words can help in rough drafts, but in final drafts, they sometimes detract from the power of the sentence. 

For example: 

> 
> This was founded. So people came. 
> 
> 
> 

is slightly less powerful than 

> 
> This was founded. People came.
> 
> 
> 

It has to do with the order of the words and such.