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I'm not really loking for an answer here, because to be honest I don't think there is one! I'm really more interested in discussing this issue with you.
Ok, they say automated submissions do not produce as effective results as manual submsissions, but where's the evidence! In my experience my results have not been 'penalised' because of automated submsissions, they just saved me a hell of alot of time and allowed me to get on with the more time consuming tasks.
Is web position gold truly the leading submission software out there? What about Top dog, search engine commando, submit wolf? They all have there pro's and cons but can anyway say that there really is a definitive, must have package out there?
The thing is submissions to search engines are a dead concept for the most part of it. You don't need to submit to the larger engines, and if so, the index page is enough.
Submission, and very carefully crafted ones, are neccessary for directories. No software can do anything for you in that respect.
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...