In other words which Senators who have served sometime between 2000 and 2014 were basically written-off for most of the campaign during their first successful Senate race, but won against the odds by being great candidates, running strong campaigns, opponents imploding, etc. I think the most interesting are ones who beat a sitting incumbent, but that's just me.
Some examples I thought of are Jim Webb (he did everything right and Allan did everything wrong), Scott Scott Brown, and Jeff Merkley. Donnelly doesn't qualify since plenty of folks thought he could be competitive against Mourdock if the latter won his primary. IIRC, Cantwell, Heitkamp, Warren, Franken, Stabenow, and Schumer were initially considered unlikely to win, but I don't remember how unlikely (i.e. were any of them actually written-off for a good chunk of the campaign).
I don't recall Gordon Smith's seat ever being considered "Safe R." It was very apparent that he would have to run as far away from George W. Bush and the national GOP as possible in order to keep his seat and he was a Republican in a state that isn't as friendly to Republicans as it was 15 years ago.
I've heard/read that Spencer Abraham was considered an incredibly ineffective senator. He was so avoidant of people on Capitol Hill that he allegedly would hide in various rooms in his offices to prevent his own staff from knowing he was there. I don't know how much of that was actually known and talked about during his reelection campaign, though.