I briefly shipped Jack with Martha, after watching her on Torchwood and on the Season 3 finale of Doctor Who, but after watching the rest of Season 3, I realized she was younger and more…young than I’d given her credit for, and the relationship started seeming too unbalanced for me.
Someone online was complaining that they overdid Martha-is-wonderful in her guest appearances on Torchwood, trying to compensate for her sometimes questionable treatment on DW. I wasn’t sure about her in my first watching of Reset, because, as the person pointed out, everyone seemed to just love her, but the second time around, I believed it. Jack obviously loved her, and if Jack loved her, the others would fall in line.
And note, the one character who doesn’t seem taken by Martha: Toshiko Sato. This is probably because the writers had already chosen her backstory, and knew she had issues with UNIT, but it fits with what I’ve noticed: Tosh isn’t as taken in by Jack as the others. She’s not going to love someone just because Jack does, whereas for Gwen, Owen, and Ianto, Jack’s feelings are enough.
And if you think Owen’s flirting with Martha had nothing to do with Jack’s adoration for her, just remember what he did the last time Jack brought a new woman into Torchwood and displayed obvious favoritism for her. Season 1 Owen was much rougher around the edges, and his treatment of Gwen was less like flirting and more like sexual harassment, but he obviously wanted her in bed, and I’m quite sure he wanted her in bed because she was Jack’s golden girl. His argument with Ianto in Death in the Death (where he says that Ianto has “won” because he goes out in the field now, and is “shagging Jack”) makes it clear that he considers having sex with someone as a way to get status, and Owen is nothing if not focused on status. Gwen was very much Jack’s golden girl in Season 1 (and still to a lesser extent in Season 2), and I’m sure that’s a large part of why Owen wanted to sleep with her. Also why he had no interest in Tosh—Owen perceived her as being below him in status, and therefore something to be avoided. Also, she’s a blatant geek, and Owen is a closet geek who associates geekiness with weakness, and will do just about anything to avoid both.