One of my users has noticed that every time he runs a backup using the cpanel interface, the server load shoots up, and gzip sucks up the CPU nearly 100% until it's completed. I ran top while he did a backup a few minutes ago and noticed that the process is not niced at all, it just sits at 0. Is there any way to force cpanel-initiated backups to nice the gzip process in order to keep the server running smoothly?

I was about to ask the same question...
My load goes up to 2.5 during the backups. It seems that it goes that high when it's gzipping a user home directory that's 1gig...

Well, I posted a topic on this on the cpanel forums, but came up pretty much empty handed. The only thing anyone there came up with is running another app that would kill off processes if they run too long, or use too much of the CPU.

I can't see if being all that hard to simply modify the command that is run when clicking that backup link to nice the process as it is being run, but i'm pretty clueless on my own.

Try submitting it as a feature request to cpanel.

The cpbackup is pretty horrible on system load and efficiency. I recommend going to http://www.rfxnetworks.com and getting his SPRI program. Once installed set gzip and cpbackup in the med setting and change the cron to run every 15min. This drastically reduced loads on our servers during the night. Backups take a little longer, but other processes can get past them now to do what they need.

just make incremental backups - not compressed - it will lower load - on second backup it will be very low.

The problem with incremental backups on some systems is Cpanel adds whatever's in the daily/weekly/monthly to the disk quota usage of each user...