Site wide links don't hurt you. It's really hard to explain what google is doing or trying to do but I'm gonna try?
Google is using your linking history to help rank you. By using a history they can use a percentage to show your websites popularity or the lack ther of.
If this month you get alot of links pointing to you, google asumes your site must be doing something good so they reward you with a better ranking and your site moves up.
Say this month you get 50% more links than you did last month. And the sites above you in the serps only did 20% more. You would move up above the ones that did less percentage than you.
But there is a line drawn that says that if your link growth percentage is higher than the average of 10% per month link growth across the entire internet then your site must be doing something spammy.
So your site drops in the rankings. Or gets a penalty or sandboxed etc...
If you have site wide links to your site, that is fine but if you take those site wides off, and you trigger your link growth percentage + or - that line that they draw that they consider average, your site will drop in the rankings. Or be penalized.
I have not seen a site become penalized for gaining links yet, but I have seen a site get completely banned from google from a decline in link popularity.
So I assume that a site that consistently gets new links pointing at it every month will continue to rise in the SERP's. But a site that gains alot of links and then loses some of those links within their percentage of what they consider the average + or - some percentage they have come up with, will be sandboxed or penalized.
This is just my theory but from reading their patent they have out, this is what I see coming in the near future if they're not allready trying it.