Because of the intensive i/o operations when downloading the blockchain and storing everything to disk, the responsivenes of the system may suffer. This is very apparent if you are running bitcoind on the same machine you're working at.
Using nice to set a lower priority for the program doesn't seem to make any difference, but using ionice, it's possible to have bitcoind do i/o operations with less priority.
This gives you the processid:
Example output:
user 19793 3.5 1.0 216244 43932 ? SLsl 04:47 0:08 bitcoind -daemon
Use the process-id, the second number to the left and set the priority for i/o operations.
This seems to do the job for me:
Check the man page for ionice to learn more about io-prioritization for programs.
But this makes the desktop usable (more responsive) again for me, while bitcoind can continue to synch the block-chain.
Hope this was useful for some.