Damn you for making me choose!
Well, from the ones I posted, Flame Race by Marco Carag is my top pick. Next would be Ambiguous Victories and Star of Polaris by PeachE.
Then there's Duel by Dan "Desvon" Adams, Last Skirmish With Vasudan Ships by Campbell March, Glory in Honor by Matthew Kenneth Diehl and of course, my own Freespace: The Great War. One day I should finish the re-editing of that thing.
Really, the only way to choose is to read them yourself. In the end, I could never choose, so I decided to post them all. And then I lost the passion I had for it. Such a shame.
BTW, you did get that e-mail I sent you, right?
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I know there is a method, but all I see is madness.