I have lot of pages which have more than one link to the home page. Is this a black mark in SEO? webgaya.
Quite natural, normally you would have a link back in your main navigation and in your footer copyright notice, nothing wrong with that.
My main site has 3 on every page, main navigation, top navigation and footer, it doesn't seem to have done me any harm
It will now do harm. Every site that is well designed uses the header, footer and sometimes the breadcrumb trail that include links to the home page and other pages within the site. You're fine and keep doing what you're doing.
Its alright to have 2-3 links back to your hme page as its normal. for instance you will have link from "Home" link, then may be have a link back from your Logo and then a footer link mentioning the name of the company or domain.