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Inktomi, Alltheweb, Teoma, Ask, Altavista, Looksmart, all give you the option of doing an XML program.
However, if you are referring to 'free submits' the days of the 'automated search engine submission software' are long gone, imho.
Every engine out there will crawl your site sooner or later, provided you have enough inbound linkage. :)
Don't bother with the submission software. They are almost completely obsolete.
Though, if somebody does ever find out which are these 'top ten' engines, if they are crawler based, it would be nice to know. :)
Ink, Google, Alltheweb, Altavista, Ask, and Wisenut = 6 crawler based engines.
If you keep digging, sure, you can find more - but Google and Ink driven traffic account for more than 95% of all my traffic - with good placement in all the others, as well.
So, based on that, I would only worry about those 2. And, if you have links to your site (as I mentioned) you will get picked up eventually.
Last time I 'submitted' to a search engine was years ago.