Maybe its a good idea to make Mark/clear seam a toggle…
I mean, either u want to clear a seam or mark it…
if its allready marked and you have an edge selected you surely want to clear it and viceversa…
what u think ? 
Peace out !
What if you select some edges that have seams and some that don’t at the same time?
How would blender know if you want to make them all seams or all non seams?
Bad idea as far as I’m concerned
If you want the toggle on/off just use the Tag Seam option rather than mark/clear seam.
Selecting all edges (A) and Ctrl/E / clear seam removes all seams in one go, this would no longer work with your suggestion.
ok…
i keep working happily 
This is there in 2.49b, I don’t think it was ported over to 2.6x. In 2.49 you can change alt+RMB select from choosing loops to tagging seams. If you pressed and held alt and than selected am edge it would be tagged as a seam if it was already a seam it would be cleared. Maybe its on that forgotten todo list.
This has been in blender since early 2.5. Select ‘tag seam’ in the toolshelf and hold down Ctrl while selecting edges to tag them.
Thanks richard I never saw it because it just says select so I always overlooked it because I kept looking for ‘loop select’ as it was previously named I didn’t even see that the label on top said edge select mode.
I also didn’t read your post carefully enough.
No, it’s there. On the tool shelf under “Mesh Options” there is “Edge Select Mode” and you can change it to "Tag Seam. Then, when you press CTRL+RMB on an edge, it will toggle its seam status. (Conversely the same works with Bevel, Crease and Sharp)
However this usage is (afaict) tied to “shortest path select”, so it only works on single edges or paths.
This raises an intresting topic and to say it with a healthy portion of sarcasm:
Are people asking for new features that are already there because they have no idea how to use their tool, or is it simply a usability failure that people can’t find the tool in the first place?
Most likely a tad of both, mixed with some missing documentation and personally I blame Blender for hiding features quite well sometimes… No room for a button? Hide several of them in a small black triangle, or make it only accessible via the spacebar menu or well… at least since 2.5 we’re context driven 
Sometimes Blender requires quite an exploratory attitude and there isn’t exactly the handbook to consult covering all functions.
But you can always read every entry in the spacebar menu, or browse through the complete list of keyboard shortcuts and try everything you don’t know yet. Time to play
In Edit mode, look in Tool Shelf under ‘Mesh Options’. Under the Edge Select Mode dropdown you have various edge tagging options. I must admit it is deviously hidden away from prying eyes.