[name]Hi[/name]! 
[name]Wren[/name]: It feels very feminine to me (I would definitely assume any [name]Wren[/name] is a girl, which I’m guessing a boy named [name]Wren[/name] would find difficult), and I agree with you that [name]Flynn[/name] and [name]Wren[/name] are pretty matchy.
You may also like [name]Callum[/name], which is Scottish for “dove.”
[name]Jonah[/name]: I think it’s a great name! It’s #137 (popular, but not too bad), but it may be very popular in your area. I can better see some of your other names with [name]Flynn[/name], though.
Names that remind of of [name]Jonah[/name]:
[name]Abram[/name]/[name]Abraham[/name] (nn [name]Bram[/name])
[name]Ezra[/name]
[name]Gideon[/name]
[name]Gabriel[/name] (oops…it’s popular)
[name]Isaac[/name] (may be too popular for you)
[name]Josiah[/name]
[name]Micah[/name]
[name]Raphael[/name]
[name]Samson[/name] (not very peaceful, though)
[name]Tobias[/name]
[name]Rafferty[/name]: I can easily see [name]Rafferty[/name] with [name]Flynn[/name] (I think it’s the best fit on your list), but if you’re not looking for an Irish theme, then [name]Rafferty[/name] isn’t the best pick…
Some names that remind me of [name]Rafferty[/name] (some Irish–sorry :-), some Scottish, Welsh, etc.):
[name]Alistair[/name]
[name]Angus[/name]
[name]Beckett[/name]
[name]Callum[/name] (means dove)
[name]Cashel[/name]
[name]Donovan[/name]
[name]Grady[/name]
[name]Rhys[/name]
You may also like [name]Raphael[/name]…
[name]Judah[/name]: I can better see [name]Jonah[/name] with [name]Flynn[/name]…
[name]Do[/name] you like [name]Jude[/name]? I can easly see [name]Flynn[/name] and [name]Jude[/name] as brothers.
[name]Rex[/name]: If you’re looking for gentle names, [name]Rex[/name] definitely isn’t gentle to me. (I think of a T-[name]Rex[/name].)
[name]Linus[/name]: I do think of Peanuts, but I think it’s a cool name.
You may also like [name]Cassius[/name].
[name]Charlie[/name]: I think [name]Charles[/name] and [name]Flynn[/name] work well together…
Names like [name]Charles[/name]/[name]Charlie[/name] and [name]Linus[/name]:
[name]Arthur[/name]
[name]Calvin[/name]
[name]Dashiell[/name]
[name]Dexter[/name]
[name]Edward[/name]
[name]Elias[/name]
[name]Elliot[/name]
[name]George[/name]
[name]Henry[/name]
[name]Joseph[/name]
[name]Maxwell[/name]
[name]Milo[/name]
[name]Oliver[/name]
[name]Peter[/name]
[name]Simon[/name]
[name]Theodore[/name]
A lot of the above are probably too popular for you, but I thought I’d still list them just in case.
Names that remind me of [name]Leo[/name] (which I love):
[name]Arlo[/name]
[name]Milo[/name]
[name]Hugo[/name]
Aside from an Irish name (or Scottish or Welsh), I can also see surnames with [name]Flynn[/name]:
[name]Archer[/name]
[name]Abbott[/name] ([name]Abe[/name])
[name]Bennett[/name]
[name]Conrad[/name]
[name]Everett[/name]
[name]Grant[/name]
[name]Graham[/name]
[name]Harrison[/name]
[name]Hudson[/name]
[name]Miles[/name]
[name]Pierce[/name]
[name]Reed[/name]
[name]Sawyer[/name]
[name]Shepherd[/name]
[name]Truman[/name]
[name]Wilson[/name]
[name]Wyatt[/name]
Best wishes to you!