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1. When Arya is stalking Varys and Illyrio:

1a. She hears water dripping in the distance.
1b. Next she observes Illyrio and Varys coming up from a vast 'well'(this is the word GRRM uses) that goes down out of sight.
1c. Varys pulls a lever and a wall descends blocking the well from sight.
1d. After the two come up, Arya trails them for quite a long distance, gradually descending.
1e. Finally she loses them, stumbles forward and finds herself at the end of a sewer emptying into the river. She dives in and swims for a while to get clean, washes her clothes, then scampers off home.

2. Varys and Illyrio are both noted for their abnormally large size, while also noted as being incredibly light on their feet. This suggests an abnormal strength.

3. Varys is noted to have a peculiar, slimy smile. This could be interpreted to mean he does not show his teeth, and that could be because he has very abnormal teeth.

4. When Tyrion threatened to throw Varys overboard, Varys retorted that he would be surprised at the result.

5. There is noted to be no bed in Vary's quarters. If he is a Merling he would likely sleep at sea or like most fish perhaps not at all.

6. Another character we know with peculiar teeth is Biter, another abnormally large man with enormous strength. The idea that this barely sentient being sat around and filed all his teeth just to scare people is absurd.

7. Varys and Illyrio both associate humans with birds, naturally as these are two lower species to them. Explains the ease with which they chop off children's tongues.

8. From their one meeting, it appears that the Merlings are experts at manipulating the humans in secret. And also there is a hint these two have plenty of patience, they seem to be comfortable waiting years for their plans to bear fruit. Perhaps they have very long lifespans or are just more patient than humans.

9. When the subject of eating people came up, Varys licked his lips.

10. Varys likely is not a Eunuch, as there is a point where he is parlaying with Tyrion where Tyrion notes that his voice seemed deeper than usual. Even if he is a Eunuch, it doesn't mean he has to be human.

11. Since he probably isn't a Eunuch, Vary's lack of sexual interest in human females is explained by being a Merling.

12. Littlefinger comes from a seafaring merchant family of Braavos and is an accomplished sailor himself, if anyone is likely to ever see the reclusive Merlings, it's the merchants and fisherman.

13. One of Littlefinger's ships is named 'The Merling King'.

14. Littlefinger claims to have Varys completely under his control.

15. House Manderly. Hugely fat, port city, can't ride a horse, they even have a Merling as their house crest. Wyman Manderly bakes Freys into pies.

16. With no readily apparent motivation, Ser Mandon Moore tried to murder Tyrion on the Blackwater. When thrown overboard, it is noted he did not scream.

17. Mandon Moore is referred to repeatedly as having dead eyes or fish eyes, and of having "no life but duty".

18. Before being attacked, Tyrion had just set Blackwater Bay on fire using wildfire which would be deadly to any creatures living underneath.

19. The Drowned God. Very handy to have a large group of humans willing to do anything for you, and it provides a ready source of spies in places of power, such as Patchface, who often tells riddles about life under the sea.

20. There is something more to Patchface, as he foretold the Red Wedding.

21. Doesn't it seem suspicious that Euron Greyjoy was so well prepared for the Kingsmoot? Almost as though he knew that this ancient ritual for selecting a ruler would resurrected -- almost as if it was done specifically for him. Perhaps Euron has been playing his brother Aeron for a fool by filling his head with "voices from the sea".

22. Davos Seaworth's visit from the "The Mother" may have actually been a siren or a mermaid. After his rescue, Davos was primed and determined to kill Melisandre. Like Aeron and Patchface, it seems Davos's drowning may have filled his head with ideas.

23. Melisandre is afraid of Patchface.

24. Brienne is told about 'squishers' by one of her companions. They are described as man eating fish people that walk on two feet.

25. If you were to give a baby the name Varys in our world today, it would mean the following: Varys - Vari - Stream; Varish - Sleeping on the Sea

26. "The storms come and go, the waves crash overhead, the big fish eat the little fish, and I keep on paddling."

27. What do Varys and Illyrio want with Dragons? This is more speculative, but consider that:
27a. When you bring Ice and Fire together, you get water.
27b. Is it as simple as this? Bring the dragons north and melt the Ice, including perhaps the entire Wall. What you have done then is raise the coastlines around the entire world. Magical global melting...
What do the merlings get out of it? Liebensraum. More ocean real estate.
27c. If the flooding were extreme enough, only a few islands would remain, places like the Eyrie.
27d. Littlefinger, "The Merling King", has made his seat the Eyrie.
27e. If this theory is correct, Littlefinger would have been made King by Merlings, giving a new take on the meaning to the ship's name.