Enigma simulator performance
Let's profile this a little bit (this is on a dual-core i7, so a bit quicker):


  Running Time  Self        Symbol Name
  
  3984.0ms  100.0%  0.0     Main Thread  0x2856c
  
  3982.0ms   99.9%  0.0      start
  
  3982.0ms   99.9%  1.0       main
  
  3936.0ms   98.7%  3081.0         crypt(char const*)
  
  640.0ms   16.0%   640.0           _platform_strchr
  
  126.0ms    3.1%   102.0           std::__1::basic_string, std::__1::allocator >::push_back(char)
  
  89.0ms    2.2%    89.0            strlen
  
  14.0ms    0.3%    14.0           DYLD-STUB$$strchr
  
  14.0ms    0.3%    4.0        free
  
  8.0ms    0.2% 1.0        szone_free_definite_size
  
  7.0ms    0.1% 7.0        DYLD-STUB$$strlen
  
  2.0ms    0.0% 2.0        operator delete(void*)
  
  2.0ms    0.0% 0.0      _dyld_start


Ok, so more than 98% of the time is spent in the crypt function (which isn't surprising really). Almost 16% of the time is spent in strchr, with another 3.1% spent in push_back. There's also a few percent (2.2) spent doing strlen. 

Ok, so how do we cut down on these:

Firstly, we'll switch over to using std::array&lt;char&gt; instead of char *. These are both stack-allocated (and so we don't incur the dynamic allocation overhead of std::string or std::vector), but std::array knows its size, and will allow us to remove the strlen in the crypt function:

#include &lt;array&gt;

const std::array&lt;char, 27&gt; alpha = {"ABCDEFGHIJKLMNOPQRSTUVWXYZ"};
const std::array&lt;std::array&lt;char, 27&gt;, 3&gt; rotors
{
    {{"EKMFLGDQVZNTOWYHXUSPAIBRCJ"},
    {"AJDKSIRUXBLHWTMCQGZNPYFVOE"},
    {"BDFHJLCPRTXVZNYEIWGAKMUSQO"}}
};

const std::array&lt;char, 27&gt; reflectors = {"YRUHQSLDPXNGOKMIEBFZCWVJAT"};
const std::array&lt;char, 4&gt; key = {"ABC"};


The indexof function then needs to change as well (and I'm going to rename it to index_of, which is easier to read):

template &lt;size_t N&gt;
std::size_t index_of (const std::array&lt;char, N&gt;&amp; str, int find)
{
    for(std::size_t i = 0; i &lt; N; ++i) {
        if(str[i] == find) return i;
    }
    return -1;
}


crypt now looks like:

template &lt;size_t N&gt;
std::array&lt;char, N&gt; crypt (const std::array&lt;char, N&gt;&amp; ct)
{
    // Sets initial permutation
    int L = li(key[0]);
    int M = li(key[1]);
    int R = li(key[2]);

    std::array&lt;char, N&gt; output;

    for ( unsigned x = 0; x &lt; N ; x++ ) {
        int ct_letter = li(ct[x]);

        // Step right rotor on every iteration
        R = static_cast&lt;int&gt;(mod26(R + 1));

        // Pass through rotors
        char a = rotors[2][mod26(R + ct_letter)];
        char b = rotors[1][mod26(M + li(a) - R)];
        char c = rotors[0][mod26(L + li(b) - M)];

        // Pass through reflector
        char ref = reflectors[mod26(li(c) - L)];

        // Inverse rotor pass
        long d = mod26(index_of(rotors[0], alpha[mod26(li(ref) + L)]) - L);
        long e = mod26(index_of(rotors[1], alpha[mod26(d + M)]) - M);
        char f = mod26(index_of(rotors[2], alpha[mod26(e + R)]) - R);

        output[x] = alpha[f];
    }

    return output;
}


which is close to what it was, but with a few minor changes (no += on a string, as we know already how large it will be and simple assign directly into that index).

And we now call it like so:

int main ()
{
    for ( int i = 0; i &lt; 1000000; i++) {
        crypt(std::array&lt;char, 37&gt;{"PZUFWDSASJGQGNRMAEODZJXQQKHSYGVUSGSU"});
    }

    return 0;
}


Let's profile this again:


  Running Time  Self        Symbol Name
  
  2873.0ms  100.0%  0.0     Main Thread  0x2c7ff
  
  2872.0ms   99.9%  0.0      start
  
  2872.0ms   99.9%  2.0       main
  
  2870.0ms   99.8%  2870.0         std::__1::array crypt&lt;37ul>
  (std::__1::array const&amp;)
  
  1.0ms    0.0% 0.0      _dyld_start


Ok, so everything except crypt has now been inlined. If we apply the modification from @MrSmith42, we shave even more time off:


  Running Time   Self        Symbol Name
  
  1855.0ms  100.0%  0.0     Main Thread  0x2ca5c
  
  1854.0ms   99.9%  0.0      start
  
  1854.0ms   99.9%  1.0       main
  
  1853.0ms   99.8%  1853.0         std::__1::array crypt&lt;37ul>
  (std::__1::array const&amp;)
  
  1.0ms    0.0% 0.0      _dyld_start


We have imposed a fairly large constraint however: we need to know the size of the string to be encrypted at compile-time (so no reading it from a file or stdin or the like). If this will always be the case, then this provides a fairly significant speed-up on my hardware.