This question comes along all too often. I'm sure you have seen the emails and websites that offer "submission to 1000 search engines for $20". This may be a very tempting proposition, in fact, for such a small amount it's worth a punt, isn't it?
This is until you realise that there are only really three search engines worth being listed in. Research recently conducted by comScore, shows that out of the 61 billion internet searches made globally in August, Google has a market share of more than 60% (37.1 billion). The nearest rivals were Yahoo! at just under 14% (8.5 billion) followed by Microsoft at 3.6% (2.2 billion); that said, the Chinese search engine Baidu.com scored 5.4% (3.3 billion) worth considering if Asia is your market.
When it comes to optimisation, taking out the 5.4% for Baidu users, if the big 3 are driving 78% of global search, the rest of the search engines have a market share collectively of only 16%. If indeed there are a 1000 search engines, anything is possible, then 996 of them have a very small share.
There is always the argument that being at the top of a little known search engine will still drive some traffic. However, the effort required to get to the top of one search engine through natural search optimisation may be the same required for a more widely used engine, and thus better served with traffic.
Not forgetting of course, you should never have to submit to a search engine. Getting listed is more about how your site interacts with others, more specifically, the links to you which are from sites that are already ranked in the search engines.