When a site links to other sites via a php-file, so that the links look like "links.php?link=1", and blocks the links.php file from spiders in robots.txt, will it raise red flags or result in penalties by the SEs?
I don't think it will lead to any penalities. Its just that the links on those pages will not be spiderable, and hence wont be of benefit to the link partners. Also, I think the page that was blocked won't have any PR passed to it.
Thanks Rosie. I'm thinking of using this for my affiliate links, so the loss of PR and 'spiderability' doesn't matter.
This is very similar to links with rel="nofollow" added to them - search engine spiders won't follow them or pass on PageRank.