I would suggest starting with measurements of the execution time of gmp's square root to establish baseline performance. Some of the foremost algorithmic and performance optimization specialists in the world have contributed to gmp, which is a mature library. Generally I would be wary of trying to compete with such a library. In fact, the Karatsuba square root algorithm by Paul Zimmermann described in the paper linked by OP is exactly what is used by the square root implementation in gmp according to its online documentation. Furthermore this algorithm has proven correctness:

Yves Bertot, Nicolas Magaud and Paul Zimmermann, “A Proof of GMP Square Root”, Journal of Automated Reasoning, Vol. 29, No. 3-4, September 2002, pp. 225-252 (online)

I don't have gmp installed to time the square root myself. Given its general nature as an arbitrary-precision library, it is possible that gmp has significant overhead for relatively short operands. Execution times beyond a few hundred cycles on x86_64 hardware would be an indication of that and provide an incentive to attempt a home-brew version.

Since OP specifically asked for "hacks", I did a quick experiment hacking code for a previous answer regarding a 32-bit integer square root into a 128-bit version. On my Intel Xeon E3 1270v2 (Ivy Bridge), with code compiled with the Intel C compiler version 13.1.3.198 at full optimization, I measure an execution time of about 440 cycles. Since both hardware and software have advanced in the past 7 years, this should undoubtedly provide an upper limit of achievable execution times.

Where a tool chain offers a native 128-bit integer type, that should be used instead of my 128-bit emulation. Also, a much better starting approximation could be used, reducing the number of Newton iterations required for full accuracy. In terms of missed micro optimizations, I had trouble with the inline assembly used to access the x86_64 instructions mul and div, in that I could not get "a" and "d" bindings to work to put operands directly into the rax and rdx registers used by those.

In standard math library practice, square roots are typically computed via Newton-Raphson (quadratic convergence) or Halley iterations (cubic convergence) of the reciprocal square root as these iterations are division-free, requiring only multiplication. However, crafting such an implementation in a robust fashion would take more time than I can afford to invest in an answer at this time.

#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>

#define MODE_INCR   (1)
#define MODE_DECR   (2)
#define MODE_RANDOM (3)

#define TEST_MODE   (MODE_RANDOM)
#define BENCHMARK   (0)

typedef struct {
    uint64_t lo;
    uint64_t hi;
} my_uint128_t;

/* lookup table for low-accuracy sqrt approximation */
const uint64_t sqrt_tab[32] = 
{ 0x0000000000000000ULL, 0x0000000000000000ULL, 0x0000000000000000ULL, 0x0000000000000000ULL, 
  0x0000000000000000ULL, 0x0000000000000000ULL, 0x0000000000000000ULL, 0x0000000000000000ULL,
  0x85ffffffffffffffULL, 0x8cffffffffffffffULL, 0x94ffffffffffffffULL, 0x9affffffffffffffULL, 
  0xa1ffffffffffffffULL, 0xa7ffffffffffffffULL, 0xadffffffffffffffULL, 0xb3ffffffffffffffULL,
  0xb9ffffffffffffffULL, 0xbeffffffffffffffULL, 0xc4ffffffffffffffULL, 0xc9ffffffffffffffULL, 
  0xceffffffffffffffULL, 0xd3ffffffffffffffULL, 0xd8ffffffffffffffULL, 0xdcffffffffffffffULL, 
  0xe1ffffffffffffffULL, 0xe6ffffffffffffffULL, 0xeaffffffffffffffULL, 0xeeffffffffffffffULL, 
  0xf3ffffffffffffffULL, 0xf7ffffffffffffffULL, 0xfbffffffffffffffULL, 0xffffffffffffffffULL
};

uint32_t clz_128 (my_uint128_t x);
my_uint128_t shl_128 (my_uint128_t x, uint32_t shift);
uint64_t udiv_128_64 (my_uint128_t x, uint64_t y);
my_uint128_t umul_64_128 (uint64_t a, uint64_t b);
int gt_128 (my_uint128_t x, my_uint128_t y);
uint64_t avg_64 (uint64_t a, uint64_t b);

/* compute integer square root by initial table lookup refined by division-based
   Newton iterations 
*/ 
uint64_t isqrt_128 (my_uint128_t x)
{
    my_uint128_t t;
    uint64_t q, y;
    uint32_t lz, i;

    if ((x.hi | x.lo) == 0) return x.lo; // early out

    // initial guess based on leading 5 bits of normalized argument
    lz = clz_128 (x);
    t = shl_128 (x, (lz & ~1));
    i = t.hi >> (64 - 5);
    y = sqrt_tab[i] >> (lz >> 1);

    // 1st Newton iteration
    q = 0xffffffffffffffffULL;
    if (x.hi < y) q = udiv_128_64 (x, y);
    y = avg_64 (y, q);

    if (lz < 106) { // 2nd Newton iteration
        q = 0xffffffffffffffffULL;
        if (x.hi < y) q = udiv_128_64 (x, y);
        y = avg_64 (y, q);

        if (lz < 86) { // 3rd Newton iteration
            q = 0xffffffffffffffffULL; 
            if (x.hi < y) q = udiv_128_64 (x, y);
            y = avg_64 (y, q);

            if (lz < 42) { // 4th Newton iteration
                q = 0xffffffffffffffffULL; 
                if (x.hi < y) q = udiv_128_64 (x, y);
                y = avg_64 (y, q);
            }
        }
    }

    if (gt_128 (umul_64_128 (y, y), x)) y--; // adjust quotient if too large

    return y; // (int)sqrt(x)
}

uint32_t clz_128 (my_uint128_t x)
{
    int r = 0;
    if (!(x.lo | x.hi)) return 128;
    if (!(x.hi & 0xffffffffffffffffULL)) { x.hi = x.lo; r += 64; }
    if (!(x.hi & 0xffffffff00000000ULL)) { x.hi <<= 32; r += 32; }
    if (!(x.hi & 0xffff000000000000ULL)) { x.hi <<= 16; r += 16; }
    if (!(x.hi & 0xff00000000000000ULL)) { x.hi <<=  8; r +=  8; }
    if (!(x.hi & 0xf000000000000000ULL)) { x.hi <<=  4; r +=  4; }
    if (!(x.hi & 0xc000000000000000ULL)) { x.hi <<=  2; r +=  2; }
    if (!(x.hi & 0x8000000000000000ULL)) { x.hi <<=  1; r +=  1; }
    return r;
}

my_uint128_t shl_128 (my_uint128_t x, uint32_t shift)
{
    my_uint128_t r;
    if (shift > 127) {
        r.lo = 0ULL;
        r.hi = 0ULL;
    } else if (shift > 63) {
        r.lo = 0ULL;
        r.hi = x.lo << (shift - 64);;
    } else if (shift > 0) {
        r.lo = x.lo << shift;
        r.hi = (x.hi << shift) | (x.lo >> (64 - shift));
    } else {
        r = x;
    }
    return r;
}

/* 128/64->64 bit division. Note: Will overflow if x[127:64] >= y */
uint64_t udiv_128_64 (my_uint128_t x, uint64_t y)
{
    uint64_t quot, rem;
    __asm__ (
        "movq %2, %%rax\n\t"
        "movq %3, %%rdx\n\t"
        "divq %4\n\t"
        "movq %%rax, %0\n\t"
        "movq %%rdx, %1\n\t"
        : "=r" (quot), "=r" (rem)
        : "r" (x.lo), "r" (x.hi), "r" (y)
        : "rax", "rdx");
    return quot;
}

/* 64x64->128 bit multiply */
my_uint128_t umul_64_128 (uint64_t a, uint64_t b)
{
    my_uint128_t r;
    __asm__(
        "movq %2, %%rax\n\t"
        "mulq %3\n\t"
        "movq %%rax, %0\n\t"
        "movq %%rdx, %1\n\t"
        : "=r" (r.lo), "=r" (r.hi) 
        : "r" (a), "r" (b) 
        : "rax", "rdx");
    return r;
}

/* macros for multi-word arithmetic */
#define ADDCcc(a,b,cy,t0,t1) (t0=(b)+cy, t1=(a), cy=t0<cy, t0=t0+t1, t1=t0<t1, cy=cy+t1, t0=t0)
#define ADDcc(a,b,cy,t0,t1) (t0=(b), t1=(a), t0=t0+t1, cy=t0<t1, t0=t0)
#define ADDC(a,b,cy,t0,t1) (t0=(b)+cy, t1=(a), t0+t1)
#define SUBCcc(a,b,cy,t0,t1,t2) (t0=(b)+cy, t1=(a), cy=t0<cy, t2=t1<t0, cy=cy+t2, t1-t0)
#define SUBcc(a,b,cy,t0,t1) (t0=(b), t1=(a), cy=t1<t0, t1-t0)
#define SUBC(a,b,cy,t0,t1) (t0=(b)+cy, t1=(a), t1-t0)

my_uint128_t add_128 (my_uint128_t x, my_uint128_t y)
{
    my_uint128_t r;
    uint64_t cy, t0, t1;
    r.lo = ADDcc (x.lo, y.lo, cy, t0, t1);
    r.hi = ADDC (x.hi, y.hi, cy, t0, t1);
    return r;
}

my_uint128_t sub_128 (my_uint128_t x, my_uint128_t y)
{
    my_uint128_t r;
    uint64_t cy, t0, t1;
    r.lo = SUBcc (x.lo, y.lo, cy, t0, t1);
    r.hi = SUBC (x.hi, y.hi, cy, t0, t1);
    return r;   
}

int gt_128 (my_uint128_t x, my_uint128_t y)
{
    return (x.hi == y.hi) ? (x.lo > y.lo) : (x.hi > y.hi);
}

int lt_128 (my_uint128_t x, my_uint128_t y)
{
    return (x.hi == y.hi) ? (x.lo < y.lo) : (x.hi < y.hi);
}

int eq_128 (my_uint128_t x, my_uint128_t y)
{
    return (x.hi == y.hi) && (x.lo == y.lo);
}

int ge_128 (my_uint128_t x, my_uint128_t y)
{
    return gt_128 (x, y) || eq_128 (x, y);
}

int le_128 (my_uint128_t x, my_uint128_t y)
{
    return lt_128 (x, y) || eq_128 (x, y);
}

/* compute average of a and b rounded towards zero, preventing overflow */
uint64_t avg_64 (uint64_t a, uint64_t b)
{
    return (a & b) + ((a ^ b) >> 1);
}

/*
  https://groups.google.com/forum/#!original/comp.lang.c/qFv18ql_WlU/IK8KGZZFJx4J
  From: geo <[email protected]>
  Newsgroups: sci.math,comp.lang.c,comp.lang.fortran
  Subject: 64-bit KISS RNGs
  Date: Sat, 28 Feb 2009 04:30:48 -0800 (PST)

  This 64-bit KISS RNG has three components, each nearly
  good enough to serve alone.    The components are:
  Multiply-With-Carry (MWC), period (2^121+2^63-1)
  Xorshift (XSH), period 2^64-1
  Congruential (CNG), period 2^64
*/

static uint64_t kiss64_x = 1234567890987654321ULL;
static uint64_t kiss64_c = 123456123456123456ULL;
static uint64_t kiss64_y = 362436362436362436ULL;
static uint64_t kiss64_z = 1066149217761810ULL;
static uint64_t kiss64_t;

#define MWC64  (kiss64_t = (kiss64_x << 58) + kiss64_c, \
                kiss64_c = (kiss64_x >> 6), kiss64_x += kiss64_t, \
                kiss64_c += (kiss64_x < kiss64_t), kiss64_x)
#define XSH64  (kiss64_y ^= (kiss64_y << 13), kiss64_y ^= (kiss64_y >> 17), \
                kiss64_y ^= (kiss64_y << 43))
#define CNG64  (kiss64_z = 6906969069ULL * kiss64_z + 1234567ULL)
#define KISS64 (MWC64 + XSH64 + CNG64)

static void error_abort (const char * filename, int line, const char *expr)
{
    fprintf (stderr, "\n%s line %d. Assertion failed: %s\n Aborting.\n", 
             filename, line, expr);
    exit (EXIT_FAILURE);
}

#define MY_ASSERT(expr)\
    ((expr)?((void)0):((void)error_abort(__FILE__,__LINE__,#expr)))

#if !BENCHMARK
int main (void)
{
    const my_uint128_t zero = {0ULL, 0ULL}, one = {1ULL, 0ULL};
    my_uint128_t x, arg, t;
    uint64_t res;

#if TEST_MODE == MODE_DECR
    printf ("Test integer square root sequentially; decrementing\n");
#elif TEST_MODE == MODE_INCR
    printf ("Test integer square root sequentially; incrementing\n");
#elif TEST_MODE == MODE_RANDOM
    printf ("Test integer square root using purely random argument\n");
#else
#error unsupported TEST_MODE
#endif // TEST_MODE

    x = zero;
    do {
#if TEST_MODE == MODE_RANDOM
        arg.lo = KISS64;
        arg.hi = KISS64 & 0x7fffffffffffffffULL;
#elif TEST_MODE == MODE_DECR
        arg = sub_128 (zero, x);
#elif TEST_MODE == MODE_INCR
        arg = x;
#endif // TEST_MODE
        res = isqrt_128 (arg);
        /* Check correctness: res * res  must be less than or equal to arg.
           (res + 1) * (res + 1) must be greater than arg.
        */
        t.lo = res;
        t.hi = 0ULL;

        MY_ASSERT ((lt_128 (arg, shl_128 (one, 127)) && 
                    le_128 (umul_64_128 (res, res), arg) &&
                    gt_128 (add_128 (add_128 (add_128 (umul_64_128 (res, res), t), t), one), arg))
                   ||
                   (ge_128 (arg, shl_128 (one, 127)) && 
                    le_128 (umul_64_128 (res, res), arg) && 
                    gt_128 (umul_64_128 (res, res), sub_128 (sub_128 (sub_128 (arg, t), t), one)))
);
        if ((x.lo & 0xffffffULL) == 0) printf ("\r%016llx_%016llx", x.hi, x.lo);
        x = add_128 (x, one);
    } while (!(eq_128 (x, zero)));
    return EXIT_SUCCESS;
}

#else // BENCHMARK

// A routine to give access to a high precision timer on most systems.
#if defined(_WIN32)
#if !defined(WIN32_LEAN_AND_MEAN)
#define WIN32_LEAN_AND_MEAN
#endif
#include <windows.h>
double second (void)
{
    LARGE_INTEGER t;
    static double oofreq;
    static int checkedForHighResTimer;
    static BOOL hasHighResTimer;

    if (!checkedForHighResTimer) {
        hasHighResTimer = QueryPerformanceFrequency (&t);
        oofreq = 1.0 / (double)t.QuadPart;
        checkedForHighResTimer = 1;
    }
    if (hasHighResTimer) {
        QueryPerformanceCounter (&t);
        return (double)t.QuadPart * oofreq;
    } else {
        return (double)GetTickCount() * 1.0e-3;
    }
}
#elif defined(__linux__) || defined(__APPLE__)
#include <stddef.h>
#include <sys/time.h>
double second (void)
{
    struct timeval tv;
    gettimeofday(&tv, NULL);
    return (double)tv.tv_sec + (double)tv.tv_usec * 1.0e-6;
}
#else
#error unsupported platform
#endif

#define N 200000000
int main (void)
{
    my_uint128_t x, zero = {0ULL, 0ULL};
    uint64_t r = 0ULL;
    int i, k;
    double start, stop;

    printf ("Running benchmark (%d iterations), please wait ...\n", N);
    for (k = 0; k < 2; k++) {
        start = second();
        for (i = 0; i < N; i++) {
            x.hi = KISS64;
            x.lo = r ^ x.hi;
            r = isqrt_128 (x);
        }
        stop = second();
    }
    printf ("r=%016llx\n", r);
    printf ("elapsed = %23.16e seconds per isqrt_128\n", (stop-start)/N);
    return EXIT_SUCCESS;        
}

#endif // BENCHMARK