The only fish I have ever had trouble getting ahold of was my silver arowana, but that was only because I went looking for them when they weren't "in season." Around here, they are most common during the spring and early summer; after that, they can be pretty difficult to find for a reasonable price, and I got mine in September (2009). I looked for maybe 2 weeks before I finally just decided to wait until spring, but then I just happened upon it while I was at an lfs looking for different fish.
My less common species where more impulse buys; although, in the case of my rarest species, the Synodontis frontosa, I had been looking at it at the lfs for over a year before I finally decided to buy it despite the insane price they were asking (it was probably the only reason they had it for so long without someone else buying it).