Umm, this is going to be a short post. The only thing that matters is the stories. Each school has a page limit (and in literary fiction the standard font is Times New Roman, not Courier). Most people submit two short stories or a novel fragment. I thought it was a good idea to apply with one mainstream story and one genre-influenced story (to show that I have range), but people have definitely gotten accepted with two genre-influenced stories. If you submit a part of a novel, it just makes good sense to submit the beginning. Can anyone really enjoy reading a middle excerpt from a novel?
The first time I applied, I jealously guarded my application stories. I revised them in secret and let no one see them. The second time, I ran both all my potential application stories through a workshop. I think that was definitely a good idea. I came close to submitting some fairly unsuitable stories (ones with guns and murder!) instead of the much more suitable ones that I ended up with. I think that before you spend however many thousand dollars on applications (and it is a really expensive process), you should probably get someone (preferably some kind of creative writing professional) to look over your stories. The way that your stories are read by a creative writing instructor will probably be much the same as the way they'll be read by an admissions committee (which is, after all, composed entirely of creative writing professors).
Okay, so, let me dispose of the other elements of the application process as well as I can.
Formatting Your Writing Sample - Most schools provide no formatting guidelines, other than that it should be double-spaced. But it seemed like the consensus amongst applicants was that they wanted 1 inch margins and twelve point Times New Roman. Since genre writers usually submit in Courier, it's worth noting that TNR fits more words on a page. Since the length restriction on writing samples is usually in terms of pages, rather than words, you should remember that a story is going to take up fewer pages once you format it in TNR.
Number Of Schools - Each school has an application fee of $40-$100. And then there is an additional fee of $23 to send them your GRE scores. This means that this is not a cheap process. Nonetheless, you should apply to as many schools as you can. I applied to a lot of schools, and I only got two funded admissions. There is a lot of subjectivity in the admissions process. It is possible to get in somewhere that is really selective and be rejected by a bunch of places that are less selective. However, for the genre-influenced writer, I will add that I applied to a bunch of schools that did not have a reputation for accepting genre-influenced writers, and I was rejected by all of them. In the end, perhaps it would have been a better decision for me to have not applied to the schools that weren't on the list in my preceding post. However, it's hard to tell. I was also rejected by a bunch of schools that have taken genre-influenced writers in the past. In the end, it probably wouldn't be a bad idea for a genre-influenced writer to take the list from my preceding post as a starting point, and subtract from it any schools that really don't appeal to you and then add any schools that, for whatever reason (location, faculty, etc.) are really appealing. It is not uncommon for MFA applicants to apply to 15-20 schools, and, honestly, that's what I would recommend (if you can afford it). However, if money is tight, I would recommend that a genre-influenced applicant should absolutely apply to at least Kansas and NCSU, since these seem like the most genre-friendly schools (that are also well-funded).
GREs - You have to take the GRE general test (but not any subject tests). Not all programs require them, but most do. In general, your GRE programs don't matter to even the slightest degree. Some schools have a minimum GRE requirement, but most don't. If you get a GRE score of below 600 (Verbal) or 1200 (combined), you might want to recheck the schools you're applying to and see whether they have minimum requirements (these requirements are usually imposed by the graduate school administrators of schools that have an inferiority complex and want to bump up their average GRE score so they'll look good in the rankings).
GPA - Also doesn't matter at all. Similar to the GRE, the graduate school administrators at some school have imposed a minimum undergrad GPA requirement of 3.0. But if you didn't have an undergrad GPA of 3.0 then what can you do? Just apply anyway. If they want you enough, they can probably find a way to admit you. Furthermore, most schools don't have this requirement.
Undergraduate Major - I wouldn't think this would matter, but, actually, a bunch of schools (Arizona State and Houston, amongst others) seemed to prefer that you have an undergraduate English major, and most MFAs that I've met seemed to have been English or Creative Writing majors as undergrads. However, most programs don't seem to care at all. Furthermore, Houston--despite their stated preference for English majors--waitlisted me, so I assume that there's similar flexibility at other schools.
Personal Statement - For most graduate school apps, your personal statement is really important, since it's your only chance to demonstrate some kind of individuality. For MFA applications, I think it is less important, since your writing sample presumably ought to be enough to separate you from the other candidates. I think the main imperative for the personal statement is to avoid coming off as crazy or arrogant. For some people (especially me!), this is really hard. There's something about personal statements that just unlocks all my craziness. I recommend that you get someone to reread your personal statement and cross out all the weirdness. When the admissions committees read your writing sample, all they want to know is that you're not going to be a pain: after all, they have to live with you for 2-3 years.
Oh, at some point in your writing sample you're probably going to want to namedrop a bunch of writers who you'd call your influences. You should probably remember your audience, and choose people that the admissions folk are likely to have heard of. You know, literary types. For instance, I chose two series of writers. The social realist types: Tolstoy, Zola, Steinbeck, Willa Cather, Sinclair Lewis, F. Scott Fitzgerald, and V.S. Naipaul. And the speculative fiction writers: Borges, Margaret Atwood, Jonathan Lethem, Aimee Bender, Stacey Richter, and Kelly Link. These are all pretty safe literary picks (well, except for Sinclair Lewis; despite his Nobel Prize, he's fallen into bad odor). I doubt you'd get much traction if you cited David Weber, Lois McMaster Bujold, Connie Willis, and Ted Chiang. One of the professors at Hopkins mentioned that he does pay attention to what authors people cite, so take that as you will...
Recommendation Letters - I don't think these matter very much, but they are by far the most annoying part of this process. If you can, you should get them from creative writing teachers or editors who can talk about your writing. Otherwise, get them from other professors or from employers (ask them to write about your general agreeability, good disposition, willingness to learn, etc.) You should definitely get the letters filed in Interfolio, which is an online credential file service that will collect your letters and mail them to schools for you (since they never let you see the letter, it remains confidential). A membership costs about $20-$30, and it costs an addition $6-8 per school, but it is absolutely worth it. If you force your professor to mail individual letters to 15-20 schools, then you are a sadist. Furthermore, professors can often be quite tardy. It's hard enough getting one letter on time. If they have to submit 15 or 20 letters, then you're guaranteed to miss deadlines.
Using Interfolio does create its own complications. It has a difficult time interfacing with the electronic application systems at most schools. Some online recommendation systems require the professor to input all this additional data (like whether you were in the top fifth percentile out of all the students they've had, or stuff like that). Since Interfolio doesn't have this data (it just has the prof's letter), they'll often refuse to submit letters to systems that have something like that. If a school offers you an address to which to mail individual letters then it is worth doing that, rather than asking Interfolio to upload the letters into their system. However, if you can't figure out a good alternative like that, then you should email the administrator at the department to which you're employing. She (it is invariably a woman) will usually be super helpful and will help you figure everything out. The only places where I had real problems submitting my letters were with NYU (which absolutely does not accept Interfolio letters, apparently), and Florida State (which is completely inflexible about not accepting paper letters). I solved these problems by not applying to NYU and by calling and begging Interfolio to force the recommendations into Florida State's system (which they eventually did).
Transcripts - Stanford is really good about mailing transcripts out for you. However some schools are not, so you should take that into account. Also, the schools will require transcripts from every post-secondary institution you've attended, so if you ever took community college classes or have other graduate degrees or something, then that can be a real pain.
Next: I have nothing more to say about MFA applications. Good luck with your applications, whoever you are. Please let me know if you have any further questions, or if any of this proved to be helpful.