Tools can eliminate a large portion of the sites from the link review list for your Google Reconsideration Request. First you want to identify all deindexed domain/pages, link networks and spammy sites that the tools will uncover. My usage tells me these are more than accurate enough to warrant their usage in reducing the number of manual reviews you do which is by far the most time consuming part of the job! Some tools are just used to collect links for review.
Using only the Google Webmaster tools list of links is likely not a good idea so you should use as many as you can afford and find. One trick I learned was to change the font color from each so when you merge the lists in excel it is clear where the dupes came from which will aid in identifying sites that were found by numerous tools which again helps in the review process. You can also find links with characteristics that mean they do not need or will need special attention during review or may well be removed immediately for example nofollow and 302ed links pass no juice so… carry on!