Certainly update the firmware to the latest:

https://www.raspberrypi.org/forums/viewtopic.php?f=28&t=243500&p=1490467#p1490467

I have been using the following settings with great success:

over_voltage=4
arm_freq=1950
gpu_freq=600
v3d_freq=750

You can verify your settings with this command:

Lakka:~ # vcgencmd get_config int
arm_freq=1950
audio_pwm_mode=514
config_hdmi_boost=5
disable_commandline_tags=2
disable_l2cache=1
disable_overscan=1
disable_splash=1
display_hdmi_rotate=-1
display_lcd_rotate=-1
enable_gic=1
force_eeprom_read=1
force_pwm_open=1
framebuffer_ignore_alpha=1
framebuffer_swap=1
gpu_freq=600
gpu_freq_min=500
init_uart_clock=0x2dc6c00
lcd_framerate=60
mask_gpu_interrupt0=1024
mask_gpu_interrupt1=0x10000
over_voltage=4
pause_burst_frames=1
program_serial_random=1
v3d_freq=750
hdmi_drive:0=2
hdmi_force_cec_address:0=65535
hdmi_force_cec_address:1=65535
hdmi_ignore_cec_init:0=1
hdmi_pixel_freq_limit:0=0x11e1a300
hdmi_pixel_freq_limit:1=0x11e1a300

You can see the current frequency values (they vary based on load) with the following commands:

Lakka:~ # vcgencmd measure_clock arm
frequency(48)=1950486272

Lakka:~ # vcgencmd measure_clock core
frequency(1)=599998528

Lakka:~ # vcgencmd measure_clock h264
frequency(28)=750001472

Lakka:~ # vcgencmd measure_clock v3d
frequency(46)=749988288

Many people are asking, how do I edit my config.txt. Do this:

mount -o remount,rw /flash
nano /flash/config.txt
mount -o remount,ro /flash
reboot

Most importantly, you want to check your temperatures:

cat /sys/class/thermal/thermal_zone0/temp

Or use the watch command to keep an eye on it and auto-update it every 2 seconds:

watch cat /sys/class/thermal/thermal_zone0/temp

With these settings, I am getting approximately 10fps more with Dreamcast emulation, and 10-25fps more with N64 emulation (at 2x resolution)