While there are lots of good ones, I only recommend two to get the job done:
1) We use the free program from www.GoodKeywords.com
to do our keyword research. Most pros swear by WordTracker, but for most people this is overkill. [oops, I just realized that was already recommended...]
2) We have a submission system that we use to submit sites by hand and share it with others at www.bfsel.com
. It's a simple system that consists of an HTML page that has links to search engines, directories, and misc resources, and an Excel spreadsheet that has the same list where you can record when and where you have submitted.
We don't use ranking or positioning, so we can't recommend anything for that, but some good ones were already listed.