Not all publishers are created alike. Before you ever write that query letter, research possible publishers. Find out the good and the bad, and narrow your choice. There are sites available to help you do this. A few of them are http://www.hipiers.com/publishing.html, http://www.anotherealm.com/prededitors/peba.htm, and http://www.passionatepen.com/romancepubs.htm
Choose a publisher in the genre you write in. If you write romance books, you may want to submit your work to an ePublisher that specializes in romance. If you submit your work to a publisher that does not accept the type of manuscript you are writing, you're wasting not only your time, but that of the submissions editor as well.
Once you've narrowed your choices, search each publisher's site. Most publishers have an FAQ (frequently asked questions) page like this one at http://www.twilightfantasiespublications.com/faq.html. Review the FAQs and the submission page, which will look a lot like this one at http://www.twilightfantasiespublications.com/submissionguidelines.html. Also, look for length requirements like these at http://www.twilightfantasiespublications.com/bookmarks.html. You'll notice that many ePublishers will accept a much shorter or much longer work that print publishers. Because ePublishers don't have to worry about page count for printing, they can often accept short stories as well as novels. Check with each individual publisher and make yourself aware of the guidelines before submitting a work.
Before signing a contract with an ePublisher, read it carefully. What rights do they demand? Most ePublishers only require the electronic rights (which gives you leave to continue your search for a print publisher). How much will they pay you? While print publishers typically only pay 10-15% royalty, ePublishers can pay from 30-40%, but be sure to note whether the publisher pays net or gross (cover price). If a publisher pays net, they take out fees before figuring the author's pay. One way to help decide if a contract is up to industry standards is to compare it with the EPIC (Electronically Published Internet Connection) contract model at http://www.epicauthors.com/contract.html