Well this is more of a "to each his own" kind of question. I can only tell you what works for me.
By default, Xfilesharing Pro uses email. This is not an organized enough option for myself.
Currently I prefer ticket solutions. There are several free options that work well that will also come with a knowledge base for your users.
http://www.uservoice.com/pricing/ is great. It's free for one agent and comes with a knowledge base. You can also add a feedback tab. All plans they have are free for one agent. Uservoice will host everything.
http://www.hesk.com/demo.php is completely free. Comes with a knowledge base, unlimited agents, canned replies, ect. You host it yourself. Next to Uservoice, this is my favorite.
http://osticket.com/features.php is pretty good. It's popular. I've used it a couple times, but something about it I do not care for. It does the job though. Free anyway.
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