After looking around in cabal2nix I think the attached patch might get Agda to 
build (with the latest mtl)

diff -Naur cabal2nix-1.33/src/Cabal2Nix/PostProcess.hs cabal2nix-1.33-new/src/Cabal2Nix/PostProcess.hs
--- cabal2nix-1.33/src/Cabal2Nix/PostProcess.hs	2012-06-03 14:25:45.000000000 -0430
+++ cabal2nix-1.33-new/src/Cabal2Nix/PostProcess.hs	2012-06-10 22:21:29.370995130 -0430
@@ -7,6 +7,7 @@
 
 postProcess :: Derivation -> Derivation
 postProcess deriv@(MkDerivation {..})
+  | pname == "Agda"             = deriv { phaseOverrides = agdaPatchPhase }
   | pname == "alex"             = deriv { buildTools = "perl":buildTools }
   | pname == "cairo"            = deriv { extraLibs = "pkgconfig":"libc":"cairo":"zlib":extraLibs }
   | pname == "cuda"             = deriv { phaseOverrides = cudaConfigurePhase, extraLibs = "cudatoolkit":"nvidia_x11":"self.stdenv.gcc":extraLibs }
@@ -50,6 +51,13 @@
                                         }
   | otherwise                   = deriv
 
+agdaPatchPhase :: String
+agdaPatchPhase = unlines
+  [ "patchPhase = ''"
+  , "  sed -i -e 's|mtl == 2.0.\*|mtl|' Agda.cabal"
+  , "'';"
+  ]
+
 cudaConfigurePhase :: String
 cudaConfigurePhase = unlines
   [ "# Perhaps this should be the default in cabal.nix ..."
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