Chiming in with a dependently typed version. First, let's get done with the boilerplate:
{-# LANGUAGE
  TemplateHaskell, DataKinds, ScopedTypeVariables,
  FlexibleInstances, PolyKinds, TypeOperators,
  TypeFamilies, GADTs, UndecidableInstances #-}
import Data.Singletons.TH
import qualified GHC.TypeLits as Lit
$(singletons [d| data Nat = Z | S Nat deriving (Eq, Show) |])
The use of TH here is purely for boilerplate reduction and we won't use TH in our actual code. In fact, the above could be (and should be) factored out in a package somewhere (at the time of writing this answer there isn't such a package with up-to-date singletons dependency).
tuplify becomes a function whose return type depends on a Nat parameter.
type family NTup n a where
  NTup (S (S Z))     a = (a, a)
  NTup (S (S (S n))) a = (NTup (S (S n)) a, a)
tuplify :: Sing n -> [a] -> NTup n a
tuplify n as = go n (reverse as) where
  go :: Sing n -> [a] -> NTup n a
  go (SS (SS SZ))     [a, b] = (b, a)
  go (SS (SS (SS n))) (a:as) = (go (SS (SS n)) as, a)
  go _                _      = error "tuplify: length mismatch"
Trying it out:
tuplify (SS (SS (SS SZ))) [1, 2, 3] -- ((1, 2), 3)
Writing out the naturals is quite arduous now, so let's introduce some syntactic sugar:
type family N n where
  N 0 = Z
  N n = S (N (n Lit.- 1))
type SN n = Sing (N n)
Now:
tuplify (sing:: SN 10) [1..10] -- (((((((((1,2),3),4),5),6),7),8),9),10)
As a side note, if we convert the empty list to () (and thereby also allow one-element nested tuples) our definitions become much more natural:
type family NTup n a where
  NTup Z     a = ()
  NTup (S n) a = (NTup n a, a)
tuplify :: Sing n -> [a] -> NTup n a
tuplify n = go n . reverse where
  go :: Sing n -> [a] -> NTup n a
  go SZ     []     = ()
  go (SS n) (a:as) = (go n as, a)
  go _      _      = error "tuplify: length mismatch"
tuplify (sing:: SN 5) [1..5] -- ((((((),1),2),3),4),5)