I recently submitted short stories to Fantasy Magazine and Clarkesworld Magazine.
I have to say, their submission system is impressive (it looks like they both use the same technology).
I wish more agents used this kind of thing for partials, etc. You put in your name, e-mail address, title of work, and cover letter, then upload a DOC or RTF for the submission itself. The system gives you a ticket number, and mails you a link to double check on the status of your submission (Open, Pending, etc.). It even tells you how many people are ahead of you in the queue.
Kudos to Fantasy Mag and Clarkesworld for making things simple for writers. Nicely done. Even though I'm one for two on rejections so far :-)