Blink emitters have a visible red LED in them in addition to the IR LED (two LEDs total) The red LEDs "blink" whenever Ir is transmitted by that particular emitter. This lets you know that everything is working, but can be somewhat distracting if you have half a dozen components with blinking red lights on them.
Also, since blink emmiters are powering 2 LEDs, they have roughly half of the IR output of a non-blink emitter. This is a non-issue unless you have equipment that needs a really strong signal to work. If you're a Xantech amplified distro box, you can also set each emitter on high or low power via a jumper, which should help you overcome and power shortcomings using blink emitters.
I personally have both single and dual blink and non-blink emitters on my system and they both work equally well. I have mouse covers on all the emitters now, so I can't see them blink anymore (and it also prevents my equipment from getting a command directly from my remote and via my IR distro system).
I recommend getting 1 blink emitter for testing purposes, You can use it as a visible indicator that stuff's working.