Source: http://en(dot)wikipedia(dot)org/wiki/Brainfuck

-,+[                         Read first character and start outer character reading loop
    -[                       Skip forward if character is 0
        >>++++[>++++++++<-]  Set up divisor (32) for division loop
                               (MEMORY LAYOUT: dividend copy remainder divisor quotient zero zero)
        <+<-[                Set up dividend (x minus 1) and enter division loop
            >+>+>-[>>>]      Increase copy and remainder / reduce divisor / Normal case: skip forward
            <[[>+<-]>>+>]    Special case: move remainder back to divisor and increase quotient
            <<<<<-           Decrement dividend
        ]                    End division loop
    ]>>>[-]+                 End skip loop; zero former divisor and reuse space for a flag
    >--[-[<->+++[-]]]<[      Zero that flag unless quotient was 2 or 3; zero quotient; check flag
        ++++++++++++<[       If flag then set up divisor (13) for second division loop
                               (MEMORY LAYOUT: zero copy dividend divisor remainder quotient zero zero)
            >-[>+>>]         Reduce divisor; Normal case: increase remainder
            >[+[<+>-]>+>>]   Special case: increase remainder / move it back to divisor / increase quotient
            <<<<<-           Decrease dividend
        ]                    End division loop
        >>[<+>-]             Add remainder back to divisor to get a useful 13
        >[                   Skip forward if quotient was 0
            -[               Decrement quotient and skip forward if quotient was 1
                -<<[-]>>     Zero quotient and divisor if quotient was 2
            ]<<[<<->>-]>>    Zero divisor and subtract 13 from copy if quotient was 1
        ]<<[<<+>>-]          Zero divisor and add 13 to copy if quotient was 0
    ]                        End outer skip loop (jump to here if ((character minus 1)/32) was not 2 or 3)
    <[-]                     Clear remainder from first division if second division was skipped
    <.[-]                    Output ROT13ed character from copy and clear it
    <-,+                     Read next character
]                            End character reading loop