My method of choice is my noggin. I don't use any software programs as I just don't think they can make the judgement calls that a human can.
They're horrid for submitting to directories. (As a guide at About and an editor at DMOZ, I can assure you that automated submissions do nothing buy annoy the heck of out the editor...)
Sure, automated programs can do a good job of rank checking, but with more and more engines publically denouncing automated checkers and Google penalizing folks that use them too often, it's not worth the risk.
I use my brain to pick the client's to get my initial ideas for keyword and market research. Then I hit the web and use sites like WordTracker to narrow those down.
Then I work with my copywriter to see where we can fit some phrases in, then we build the content, then I submit by hand to engines and directories and use an Excel spreadsheet to track link campaigns.
So I guess i like software (Excel, WordTracker) but not automated ones...