Always try the latest version, available here:
https://github.com/snes9xgit/snes9x/releases
The libretro version in RetroArch's core tracker is generally up-to-date, so it is safe to use as well.
If you need a better performing version, you should use the libretro Snes9x-2010 core. This is preferred over using old standalone versions of Snes9x, because those versions are missing many fixes that libretro contributors have backported to their core.
If you want to run the games that Snes9x doesn't support, or simply don't like Snes9x's user interface, bsnes and higan are both great options.
You may notice that some people peddle older versions like 1.52 or 1.43. Here's why:
1.43
This is an ancient version that has really low CPU usage, so it tended to be used on very slow devices. There is no reason to use this with a modern device.
1.51
This is the last version without proper sound emulation. Sound effects can't be produced properly with this version, so there is no reason to use it.
1.52
This was the last version without close HDMA and IRQ timing, so people prefer it for speed.
1.53
This was the last version using Blargg's S-SMP core. It also added more accurate IRQ timing, so was more CPU intensive. This performance loss has been mostly mitigated.