Jesus, Nikolay Davydenko comes to mind. He finished each year from 2005 to 2009 in the top 6, including #3 in 2006, but never seemed like a real threat to win a Slam (his highest finish was a SF, which he did multiple times). Nikolay had the misfortune of peaking at the same time as Federer.
Ljubicic is another. His highest year-end was #5 but he did make it to #3 that year. I don't think he was a real threat to win a Slam.
Going back a bit, Alex Corretja comes to mind. While he was an excellent player for a few years and a good example of how if you don't win a Slam no one remembers you after a few years. But he finished 1998 at #3 and I don't think was considered a serious contender for a Slam, although he did make it the Final of the French Open twice, losing to Moya and Kuerten.
I know he won a Slam, but I can't help but think of Michael Chang. Chang won the French Open at the tender age of 17 and played until he was 31, but when Sampras and Agassi rose to dominance, I don't think anyone considered him a serious threat to win a Slam. He did make three more Finals, losing to Muster, Becker and Sampras, but only one went past three sets (Becker). Chang did win seven ATP 1000-level tournaments, so maybe at the time he was viewed as more of a threat, but in hindsight he seems like the 90s version of what David Ferrer has been the last few years - the most consistent of the near-elite, but possibly the least threatening to upset one of the elite players.