That may just be your problem, Bao-Dur is close to impossible to convert as a DS char. As LS it's pretty easy.
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To get Bao-Dur to go to the Dark Side, you have to respond to him like you're Light Side until you've built up enough influence with him. Note that you WILL have to get Light side points to get influence with him. When I did it I helped the plagued refugee on Nar Shadaa (with only him in the party) and helped the trappped Mandalorian recruit on Dxun (also with only him in the party). Both times he reacts to you if you did the "good-guy" thing and you must respond as a good guy would to get influence. It took both of those things as well as using the Light Side responses to his conversation options to get enough influence to set him on the Dark path. Once you have enough influence he'll tell you about the anger that's built up in him over the years and you offer to help him use that anger for strength and he becomes a Dark Jedi Guardian. It's MUCH easier to make him a Light Jedi of course.
As for the original question, I usually use either something like Krath Holy Armor or Exar Kun's battle armor, usually with some +defense overlays and strengthing underlays. I make sure to get him powers that aren't restricted by armor.
To the guy that said Bao-Dur makes the best unarmed fighter... I disagree, he's a grear fighter if you spec him out right, but not the best at unarmed. That distinction goes to the Handmaiden (who also happens to be the best NPC fighter you can get IMO) She get's the Echani fighting moves that're pretty nice. I usually keep her on the ship til I'm level 17 and can make her a Jedi (you just have to duel her three times and she won't fight you the third time til you're 17). In other words she's Soldier 6/Jedi Guardian 10 to begin with. After that she's by far the best fighter and I usually keep her with me all the time. The Disciple is pretty decent if you're playing a female, but the Handmaiden is MUCH better, especially since she teaches you Battle Precognition (adds your Wisdom mod to your defense)