One niggle Ive had with Gnome for a while is that when I click a link in Icedove (Debians name for the Thunderbird mail program) it loads the page in Epiphany, the Gnome browser, instead of Iceweasel (Debians version of Firefox).
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Program associations are handled via the update-alternatives program which must be run as root. In Debian, programs register themselves as alternatives to perform the same actions. Debain will choose an alternative by default but if you want to change it you can use the command line program.