6 months after Penguin - What are safe now?

I got hit by the Penguin update in around February and March. I did everything for my sites then but they have never recovered. I basically gave up on them and have been away from SEO.

Now I have launched a new site a month ago but I have been hesitant of doing any kind of SEO because I really don't know what effective now and what not. Not being effective is still OK but I have been afraid of doing anything dangerous.

After Penguin updates, I heard many different opinions/ideas in regard to what's safe or still effective and what's not. I haven't kept up and things must have changed a lot in this 5-6 months too and some discussions must have settled to a certain extent as well. So I'd like to know what are general opinions at this point.

I'm especially interested in these points below. For example, In February or March, Google was cracking down "unnatural links" but still Link Wheel or Link Pyramid were safe. But people were starting to say Link wheel was dangerous because there are more foot prints etc. I also heard Google was starting to crack down on Link pyramid as well. So what I'm wondering are

*Link Wheel, Link pyramid and if safe any precautions when using them?
*Blasting to the first tier (not the money site - its dangerous, but the tier next to the money site. It is related the above)
*Directories (I heard it started to be ineffective?)
*Article submissions (there were a lot of discussions going on about it and also about the effectiveness especially on spinning)

If you can think of any other points or changes and mention them, I would appreciate it. I basically want to know the digest of changes in SEO for past 5-6 months.

Thank you.