Building links manually can also be considered spam.
"Any links intended to manipulate a site's ranking in Google search results may be considered part of a link scheme." ~ Google
Building a random blog, posting a link on it to your site, and then never touching it again is the same thing as using a tool that does it...except much, much slower. No idea why people think it's any different. It is spam. It's against the Google Webmaster guidelines.
Low quality directory or bookmarking sites are also considered spam. Just because you build it manually is no different.
And we have a great example here...
"Forum comments with optimized links in the post or signature"
Originally Posted by cssbutton
i advice you build your links manually to avoid google penalizing you.