TheMadScientist - 5:52 pm on Aug 19, 2010 (gmt 0)

I think this is a great topic, but could you expand on a few of them?

-- Having no-follow tags to affiliate links
How does this one hurt?

Extra links (with or without) nofollow dilute your PageRank and keep it from being spread to your pages, but a link is a link as far as this goes, so I'm not sure on the specifics here? You 'dilute' your internal PR as much with a nofollow link as a follow link, so there could be an issue, but it's not a penalty... It's just diluted PR.

I use this type of link on a site and haven't had any issues.

Too Many Affiliate Links?
Definitely, either follow or nofollow though.
(Of course 'too many' is totally subjective and site specific.)

-- Changing site templates
From what I've read here, this usually correlates with internal nav and 'page load order' changes, which are IMO more 'ranking changers' than the look and feel.

-- Modifying Title, Descriptions...
Titles yes, but descriptions?
How do they effect your rankings... They aren't used by Google for rankings AFAIK.

IMO Descriptions have a much greater impact on click-thru than rankings directly, and I think click-thru could effect your rankings, so they may have an indirect effect, but I'm not sure how changing them could have a direct effect on your rankings and I'm not sure how you would know if it is positive or negative until you've tried it and seen if you can generate more clicks through the changes?

-- internal 301 redirects?
Use a bunch (some would say too many lol); have for years; haven't had any issues.

Sorry to not directly add to the list, but not sure on some of the list of things you have and don't want to have people scared into not making a change, so I think expanding on how some of them are seen as harmful would be good, because my experience / knowledge seems to be different.