Some links are obviously bad, others might be harder to figure out.
It will take some time to analyze those links, but it will be worth it (especially if you have a manual penalty against you already).
Let’s talk about some tools you can use to analyze those backlinks of yours.
Open Site Explorer — This tool will give you URL, domain authority, page authority, and title of your links. You can also check for and analyze recently discovered links, top pages, and linking domains.
Google Webmaster Tools — Yep, you can use this Google tool for this (you are doing something Google wants you to do). Go to the “Traffic” section of your site and download any inbound link data.
MajesticSEO — This nice link profile analysis tool shows you things like anchor text and types of links, and also assigns a trust score.
AHrefs — You can view inbound links according to domain, type of site, TLD suffix, IP, as well as types of links, such as: redirects, nofollow/dofollow, sitewide, and more).
Link Research Tools — All kinds of tools, ranging from link profilers, missing links, checking and monitoring of links, and a link detox tool that scans for suspicious or bad links for you.
The main goal is to compile a list of current backlinks that have the following information, at a minimum:
Page linked to (on your site, that is).
The URL linking to your site.
Anchor text used in the link.
Anchor text distribution for your site (brand, long-tails, URL, etc).
If the links are nofollow or dofollow.
Home page links.
As a side-note: if you only or mostly have links to your homepage, you need to build links that go deeper into your site (sub-pages) and if you hardly have any “brand” links (like your website name, business name, etc.) then you should beef up on that end, too.