Combinatorics: In my opinion, Discrete Mathematics is only a mediocre journal (I wouldn't consider this top journal). Yes, it contains good papers, but it contains a lot of papers... on average... it's average.
Some other ones worth a mention (on top of JCTA, JACO and EJoC mentioned earlier): Journal of Combinatorial Theory Series B, Journal of Combinatorial Designs, Annals of Combinatorics, Combinatorica.
The Electronic Journal of Combinatorics should probably go on the top list in combinatorics, but since it's a free, open access journal, it's usually assumed to be worse than it actually is.
Combinatorics, Probability, and Computing, the Journal of Graph Theory and the Electronic Journal of Combinatorics seem to be widely regarded as excellent journals, at the level of the ones mentioned above (except Discrete Mathematics).
Formerly, the "Journal of Combinatorics" does not really exist -- I'm told it used referred to be a printed version of the "Electronic Journal of Combinatorics"Combinatorics" (which has led to some confusion, see e.g. http://symomega.wordpress.com/2010/03/30/the-arc-the-era-and-the-ejc/), although most people in combinatorics haven't even heard of it.
In fact, due to this confusion, the Electronic Journal of Combinatorics has been mis-labelled by the ARC as a C journal (as bad as it gets) -- AustMS regard it as an A journal (
Joel Reyes Noche's comment points out that there is a higher ranking, A*, currently achieved by JCTA/JCTB). I'm told this is based on citation statistics for the new journal entitled "Journal of Combinatorics"Combinatorics".See Gordon Royle's blog for some comments: http://symomega.wordpress.com/2010/03/30/the-arc-the-era-and-the-ejc/ [CMSA are pushing for this to be fixed in the next round of journal rankings, fingers crossed]