What is the significance of blinking systems on the galaxy map?

Blinking indicates that you currently have an active mission in your log to complete there.

If you see no obvious mission, scan around the system and you should find a war asset or fuel depot to recover.

I have a system always blinking too, About 10 o'clock if the milky way were a clock, near the outside of the sector with the Citadel. called Minos Wasteland. For me it's currently at 100%, no missions. I went there anyway and found two systems, one called Fortis, the other Arrae, and both are 100% explored with no active missions in either. A glitch maybe? That seems to be the only one for me currently outside my only other active mission.

To add one more thing, if you pick up on conversations around the Citadel people ask you to find crap for them (or you eavesdrop about it...) Sometimes systems with the items they require will blink too. These won't be 100% explored, but I'm not sure if you can find the item before gaining the quest...