1script - 6:13 pm on Jun 28, 2012 (gmt 0)
So my question is why do some sites get penalized for them? What makes the difference?
My guess would be the ratio of bad links vs good ones? Problem with bad links is that you usually acquire them en masse, which is I think partly what makes them bad in Google's eyes in the first place. Conversely, you acquire good links individually, so they take time to accumulate. In other words, the ratio of good vs. bad is very easily tipped towards bad ones, can happen virtually overnight.
If I can use my sorry story as an example, I have been sponsoring those WP themes for a few months back in 2009 and there's probably 15-20 of them out there (never kept record - what a stupid mistake) that have links in the footer pointing to my sites. One link per a theme of course, but I did various themes for several sites. This was never a very effective tactic because not many people were using them, so not too many links were created this way. Somewhere along the way I've stumbled upon a great designer that was making nicer looking themes and was actually promoting the theme. Not much was happening initially anyhow, and I've stopped the practice and essentially forgot about it.
All of a sudden, 2 years later I've found that some of the nicer themes were used for many blogs, (most of them spam autoblogs) and tens of thousands of links created this way and I think that's what has tipped the scale.
Anyway, I think they may use different criteria but the bad/good ratio is probably the most telling and easily computed one.