|Proper Way to Place Link|
Should you place link in footer / shared border or just within webpages?
I have several sites with different content. Currently, I put links to these partner sites in the footer / shared border so they appear on all webpages within one site. But I wonder if this will cause any problem with the search engine (especially Google). If 100 pages of Site A all link to Site B in the footer, will I get any penalty? Should I just add the link to partner sites on the index page?
Don't just think about search engines, think about your visitors. Will a great mass of links appeal to them? I doubt it.
Much better, once the site starts growing, to be a bit more flexible with your menus.
For example, on sme of my sites, I use two menus; one is to 'section indexes' and appears on every page, the other is a 'local menu', linking to pages within that section.
It maintains a logical naviagtion system, which makes life easier for SEs and for visitors - and keeps each page fairly 'clean' not cluttered, confusing and aggressive.
No point in frightening visitors away - human or SE!
"For example, on sme of my sites, I use two menus; one is to 'section indexes' and appears on every page, the other is a 'local menu', linking to pages within that section."
I do the same thing too. Some main pages are accessible from the main menus which appears on all pages. Secondary pages are accessible from the main pages only.
As for the links to partner sites (only 3 sites), if I think of the visitors, I would think that it is better to leave them on the footer/shared border. Some people may enter other content pages (not index page) and if they see my partner sites on those pages, they may follow the link and check out my other sites. The problem is I don't know if there is a problem with the search engine as they may think that you are artificially creating more inbound links to the other sites.
Depends what you mean by 'partner sites'.
If they are reciprocals from non-related sites, you could be in trouble. Even if they are relevant, a link from every page may look suspicious to google.
The ONLY safe way to assess link is to consider human visitors first, last and always.
If a site is useful to them, and recommended by you, then that link is as safe as houses*. However, how many links will your visitors REALLY need to see on every page?
If you cannot answer that, then don't be sure the SEs can, either :)
*Earthquake zones excepted.