The solution is to use the URL encode equivalent for the comma which is %2C.
[div style="margin-left:5.5em; text-indent:-4em"]Before: [font style="color:#000099;"]http://www.ynetnews.com/articles/0[font style="color:#ffffff; background-color:#3366cc;"],[/font]7340[font style="color:#ffffff; background-color:#3366cc;"],[/font]L-4245879[font style="color:#ffffff; background-color:#3366cc;"],[/font]00.html[/font]
[div style="margin-left:5em; text-indent:-3.5em"]After: [font style="color:#000099;"]http://www.ynetnews.com/articles/0[font style="color:#ffffff; background-color:#3366cc;"]%2C[/font]7340[font style="color:#ffffff; background-color:#3366cc;"]%2C[/font]L-4245879[font style="color:#ffffff; background-color:#3366cc;"]%2C[/font]00.html[/font]
If you copy that URL text with the %2C encode characters and use it in a [link] tag, it should work as expected.
For the other problem characters with URLs in the [link] tag, see this part of a post of mine in this forum:
[div style="margin-left:1.5em;"]http://www.democraticunderground.com/?com=view_post&forum=1256&pid=1695#chars_in_link_address
That post actually lists most of the problems and solution to the majority of issues with links and the [link] tag.