What the heck? There is no reason that a software tool can't be used for all of your links. There is no way for google to determine if a link got created manually or with a software. It simply depends on how you use them.
My recommendation:
T1 links:
HIGH Quality article with sentence and paragraph spinning uploaded on trusted web2.0 profiles (profiles which already have content posted which doesn't promote your site plus curated content from high authority sites)
T2 links:
Quality article with word, sentence and paragraph spinning on web2.0, article directories, wikis, pdf sharing etc.
T3 links:
Blog comments, and all the before mentioned, just with crap spun content.
For T1 and T2, I also recommend to use social signals
Tools I'd recommend based on my own experience (note: There are many ways, this is just what I use!)
Zsubmitter for web2.0 sites (currently testing, but it looks really refreshing and I'm impressed so far.)
Scrapebox
Blognetbandit 3.0
addmefast bot (there is a free one in the forum!) for social signals.
SENuke/Licorne AIO are also nice to have, even though I prefer the first three tools I mentioned to create my backlinks.
warm regards,
Michael