Hi Alfred,
if I mine the logfiles and only deindex stuff that Google sends no further traffic to after a year could this be seen as trying to game the algo or similar?
No, this wouldn't be seen as gaming the algorithm. All you are doing is finding those pages that are serving no purpose and removing them.
if the articles are noindexed but still exist, is that enough to escape a Panda penalty or does the page need to be physically gone?
There are two thoughts on this. The noindex route is seen as the more gentle way to see if this fixes things for Google - in my experience, it is generally not enough.
What you need to remember is that even if you noindex a page, Google can still apply a penalty based on the page existing as the content can still be seen / crawled. There is no hard and fast rule to say they will, but it is a real possibility.
The advice to my customers is generally to remove the pages in question to avoid all possible doubt. Find the pages that are not delivering benefit to the site or visitors and start there.
I would be advising you undertake a content audit to fully assess the site and what really needs to be done. There is little point in killing lots of pages if it isn't lots of pages causing you issues.
-Andy