Updated with new functions and additional timings
Since this question inspired so many answers I think there is as need to compare them.
I have included two of my own functions, freely borrowing from previous answers:
wizard1[] :=
Inner[Compose, sel /. {True -> f, False -> Identity}, list, List]
wizard2[] :=
Module[{x = list}, x[[#]] = f /@ x[[#]]; x] & @
SparseArray[sel, Automatic, False]@"AdjacencyLists"
(wizard1 may not work as expected if list is a matrix; a workaround is shown in that post.)
Notes
These timings are conducted with Mathematica 7 on Windows 7 and may differ significantly from those conducted on other platforms and versions.
Specifically I know this affects Leonid's method, as Pick has been improved between versions 7 and 8. His newer form with Developer`ToPackedArray@Boole is slower on my system so I used the original.
Rojo's first function had to be modified or it fails on packed arrays, but I believe this affects other versions as well.
kguler's method list /. Dispatch[Thread[# -> f1 /@ #] &@Pick[list, sel]] does not produce the correct result if there are duplicates in list and was omitted from the timings.
Timings with symbolic (undefined) f
Here are timings for all functions when f is undefined:

$x$ is length of list; $y$ is average time in seconds. We can see that all the methods appear to have the same time complexity with the exception of one, the line at the top on the right-hand side. This is MapAt[f, list, Position[sel, True]] at it makes quite clear "what's wrong with" this method. The warning on this page regarding MapAt rings true.
Timings for 10^5 in the chart by rank are:
$\begin{array}{rl}
\text{wizard2} & 0.02248 \\
\text{ecoxlinux2} & 0.02996 \\
\text{wizard1} & 0.03184 \\
\text{leonid} & 0.03244 \\
\text{simon} & 0.03868 \\
\text{ruebenko} & 0.04116 \\
\text{artes3} & 0.0468 \\
\text{rojo3} & 0.04928 \\
\text{verbeia} & 0.05744 \\
\text{rm2} & 0.0656 \\
\text{rm1} & 0.0936 \\
\text{artes2} & 0.0936 \\
\text{artes1} & 0.0966 \\
\text{jm2} & 0.106 \\
\text{rojo2} & 0.1154 \\
\text{rojo4} & 0.1404 \\
\text{kguler4} & 0.1434 \\
\text{kguler2} & 0.1496 \\
\text{kguler1} & 0.1592 \\
\text{jm1} & 0.1654 \\
\text{rojo1} & 0.3432 \\
\text{ecoxlinux1} & 19.797
\end{array}$
Timings with a numeric compilable f
For an array of 10^6 Reals and with f = 1.618` + # & timings are:
$\begin{array}{rl}
\text{wizard2} & 0.04864 \\
\text{leonid} & 0.2154 \\
\text{ecoxlinux2} & 0.452 \\
\text{ruebenko} & 0.53 \\
\text{artes3} & 0.577 \\
\text{simon} & 0.639 \\
\text{wizard1} & 0.702 \\
\text{rojo3} & 0.811 \\
\text{rm1} & 0.982 \\
\text{verbeia} & 1.014 \\
\text{artes2} & 1.06 \\
\text{artes1} & 1.123 \\
\text{rojo2} & 1.279 \\
\text{rm2} & 1.357 \\
\text{jm2} & 1.45 \\
\text{rojo4} & 1.747 \\
\text{kguler4} & 1.841 \\
\text{kguler2} & 1.934 \\
\text{kguler1} & 2.012 \\
\text{jm1} & 2.106 \\
\text{rojo1} & 3.37
\end{array}$
We're not done yet.
Leonid wrote his method specifically to allow for auto-compilation within Map, and my second method is directly based on his. We can take this a step further for a Listable function or one constructed of such functions as is f = 1.618` + # & by using f @ in place of f /@ as described here:
Module[{x = list}, x[[#]] = f @ x[[#]]; x] & @
SparseArray[sel, Automatic, False]@"AdjacencyLists" // timeAvg
0.03496
Refrence
The functions as I named and used them are:
ruebenko[] :=
Block[{f},
f[i_, True] := f[i];
f[i_, False] := i;
MapThread[f, {list, sel}]
]
artes1[] :=
(If[#1[[2]], f[#1[[1]]], #1[[1]]] &) /@ Transpose[{list, sel}]
artes2[] :=
If[Last@#, f@First@#, First@#] & /@ Transpose[{list, sel}]
artes3[] :=
Inner[If[#2, f, Identity][#] &, list, sel, List]
ecoxlinux1[] :=
MapAt[f, list, Position[sel, True]]
ecoxlinux2[] :=
Transpose[{list, sel}] /. {{x_, True} :> f[x], {x_, _} :> x}
rm1[] :=
Transpose[{list, sel}] /. {x_, y_} :> (f^Boole[y])[x] /. 1[x_] :> x
rm2[] :=
Transpose[{list, sel}] /. {x_, y_} :> (y /. {True -> f, False -> Identity})[x]
rojo1[] :=
With[{list = Developer`FromPackedArray@list},
Normal[SparseArray[{i_ /; sel[[i]] :> f[list[[i]]], i_ :> list[[i]]}, Dimensions[list]]]
]
rojo2[] :=
Total[{#~BitXor~1, #} &@Boole@sel {list, f /@ list}]
rojo3[] :=
If[#1, f[#2], #2] & ~MapThread~ {sel, list}
rojo4[] :=
#2 /. _ /; #1 :> f[#2] & ~MapThread~ {sel, list}
jm1[] :=
MapIndexed[If[sel[[Sequence @@ #2]], f[#1], #1] &, list]
jm2[] :=
MapIndexed[If[Extract[sel, #2], f[#1], #1] &, list]
verbeia[] :=
If[#2, f[#1], #1] & @@@ Transpose[{list, sel}]
kguler1[] :=
MapThread[(#2 f[#1] + (1 - #2) #1) &, {list, Boole[#] & /@ sel}]
kguler2[] :=
(#2 f[#1] + (1 - #2) #1) & @@@ Thread[{list, Boole@sel}]
(*kguler3[]:=
list/.Dispatch@Thread[#->f/@#]&@Pick[list,sel]*)
kguler4[] :=
Inner[(#2 f[#1] + (1 - #2) #1) &, list, Boole@sel, List]
simon[] :=
Block[{g},
g[True, x_] := f[x];
g[False, x_] := x;
SetAttributes[g, Listable];
g[sel, list]
]
leonid[] :=
With[{pos = Pick[Range@Length@list, sel]},
Module[{list1 = list},
list1[[pos]] = f /@ list1[[pos]];
list1
]
]
wizard1[] :=
Inner[Compose, sel /. {True -> f, False -> Identity}, list, List]
wizard2[] :=
Module[{x = list}, x[[#]] = f /@ x[[#]]; x] & @
SparseArray[sel, Automatic, False]@"AdjacencyLists"
Timing code:
SetAttributes[timeAvg, HoldFirst]
timeAvg[func_] :=
Do[If[# > 0.3, Return[#/5^i]] & @@ Timing@Do[func, {5^i}], {i, 0, 15}]
funcs = {ruebenko, artes1, artes2, artes3,(*ecoxlinux1,*)ecoxlinux2,
rm1, rm2, rojo1, rojo2, rojo3, rojo4, jm1, jm2, verbeia, kguler1,
kguler2,(*kguler3,*)kguler4, simon, leonid, wizard1, wizard2};
ClearAll[f]
time1 = Table[
list = RandomInteger[99, n];
sel = RandomChoice[{True, False}, n];
timeAvg@ fn[],
{fn, funcs},
{n, 10^Range@5}
] ~Monitor~ fn
f = 1.618 + # &;
time2long = Table[
list = RandomReal[99, 1*^6];
sel = RandomChoice[{True, False}, 1*^6];
{fn, timeAvg@ fn[]},
{fn, funcs}
] ~Monitor~ fn
MapAt[f, list, Position[sel, True]]? – ecoxlinux Aug 23 '12 at 22:58