There are many instances in life when we ABUSE our own work and ask one question to God, WHY ME? Lets say, one fine morning you come to your office in a fresh mood. You work as an SEO and its your habit (it should be) to visit Google webmaster for all your clients. You are sitting on your chair and listening a song or blowing a whistle. While webmaster is logging in you are remembering your weekend and all the fun you did with your friends. 
What next? You came across a notification in one of your client website/or your own website and all your fun you did on weekend, your whistle, your song, your mood, etc. vanished in a second. You think that this world is no more for you. You start thinking about what will you do now. Your bosses or clients will ABUSE you as much as they can. You prepare yourself to get ABUSED. One question you will ask from god is that, WHY ME? WHY YOU CHOSEN ME ONLY? WHY YOU ALWAYS BEATS ME WITH YOUR STICK? and you start remembering all bad things happened with you before and you conclude that you have the worst luck than any one else in this world.
All this messed story above is due to one terrifying notification you saw in Google webmaster tools about your website penalty. It is the worst message/notification one can expect. 
So, coming to the point below is a great resource created by BRUCE CLAY INC. about doing link evaluation and how to deploy the process. If you are struggling with thousands of back links of your penalized website and don't know what to do, have a look below and follow the Flow Chart. I used it and I swear it works great as time is money and it saves loads of money.