I am not a fan of programs to automate the process. I see too much risk involved when something leaves you hands. THe best program i have found for managing link building is Excel. Just create a spreadsheet to track what you have done or are doing. There are some programs out there that can help your on page optimization but as far as off page I would stick to doing it yourself. It takes longer but you keeps out of that muddy link-exchange, link-farm area.