The following is my personal (i.e., includes all of my mathematical prejudices) ranked list of subject area journals in number theory.
From best to worst:
1) Algebra and Number Theory
2) International Journal of Number Theory
3) Journal de Theorie des Nombres de Bordeaux
4) Journal of Number Theory
5) Acta Arithmetica
6) Integers: The Journal of Combinatorial Number Theory
7) Journal of Integer Sequences
8) JP Journal of Algebra and Number Theory
For a slightly longer list, see
http://www.numbertheory.org/ntw/N6.html
but I don't have any personal experience with the journals listed there but not above.
Moreover, I think 1) is clearly the best (a very good journal), then 2)-5) are of roughly similar quality (all quite solid), then 6) and 7) have some nice papers and also some papers which I find not so interesting, novel and/or correct; I have not seen an interesting paper published in 8).
But I don't think that even 1) is as prestigious as the top subject journals in certain other areas, e.g. JDG or GAFA. There are some other excellent journals which, although not subject area journals, seem to be rather partial to number theory, e.g. Crelle, Math. Annalen, Compositio Math.
Finally, as far as analytic and combinatorial number theory goes, I think 4) and 5) should be reversed. (Were I an analytic number theorist, this would have caused me to rank 5) higher than 4) overall.)
I somewhat disagree with some of the earlier answers on the "jobs applications impact". First, I think it makes absolutely no difference whether you have "submitted to Annals" or "preprint" on your CV. Everyone knows the acceptance chances and will ignore this line. Second, it is really important that all your papers are available on the arXiv or your personal web page. Often, the hiring committee can't judge the applicant's work, and will ask a local expert at the department to take a look at the papers and give an impartial opinion. If the papers are not available, the committee is forced to trust the applicant on their existence, a bad situation all around. Finally, except for the really top journals, having a paper published vs. having it still in a preprint form is of minor difference - if the local experts and/or reference letters are all saying that these recent papers are really good, that's sufficient. From that point of view, you should basically ignore the job application considerations, and always do what's best for the paper.
P.S. If I may make a suggestion, I think it's much more important to choose the right people to write reference letters than worrying about minor points in your CV. Especially now, in the mathjobs era of mass applications, it is the letters that really help people stand out from the crowd. So my advice would be to start thinking well in advance who can you ask for the letters, and learn how to better communicate your results (to them and everyone else).
Best Answer
It's perhaps not in the spirit of Noble Academe, but increasingly I find myself looking at the editorial board for the journal. If there are people on it with whom I have actual personal professional contact (e.g. discussion at conference, or a prior exchange of work ideas) then -- other things being equal -- I'll be more likely to submit there.
(This is just for those of us whose primary concern is to aim for a decent journal but avoid the immediate "bin-as-intray". If your work is good enough, this shouldn't matter as much.)