Had a lot of problems with clicking sounds when playing from my NFS share on my server.
After some googleing I found that a lot of people report that the clicking sound appear when network traffic is apparent.
Decided to try to experiment with MTU size, and found that if I set MTU to 1492 or 746, the clicking dissapeared.
Even when playing 24/192 from my server, there is no clicking at all. (This is re-sampled to 24/96 in my poor little raspberry because max input rate on my Hegel HD2 is 24/96).
My raspberry is overclocked to 1GHz, and uses 50-70% CPU when resampling from 24/192 to 24/96.
When playing 24/96 directly, it uses 6-7% CPU.

From one noob to another:
log on to your raspberry (via ssh if you are running linux, or use putty if you are running windows).
run the command: ifconfig eth0 mtu 746
If this does the trick for you, you can edit your interface config, so it will be set at boot.
To edit the file, run the command: nano /etc/network/interfaces

EDIT:
My interfaces file looks like this:

auto lo
iface lo inet loopback

auto eth0
mtu 746
iface eth0 inet dhcp

auto wlan0
iface wlan0 inet dhcp

ok.
I did not change anything in my router. The default MTU there is 1500.
I am running NFS now. Have not tried Samba after I changed MTU to 746. Will try later….

this is my ifconfig output:

eth0 Link encap:Ethernet HWaddr b8:27:eb:1d:7e:aa
inet addr:192.168.1.147 Bcast:192.168.1.255 Mask:255.255.255.0
UP BROADCAST RUNNING MULTICAST MTU:746 Metric:1
RX packets:2589943 errors:0 dropped:0 overruns:0 frame:0
TX packets:161533 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:3638454859 (3.3 GiB) TX bytes:28069815 (26.7 MiB)

this is my alsa output:

[email protected]:/etc/network# cat /proc/asound/card0/pcm0p/sub0/hw_params
access: RW_INTERLEAVED
format: S24_3LE
subformat: STD
channels: 2
rate: 96000 (96000/1)
period_size: 12000
buffer_size: 48000