I use ZIP, using -9yrS. There are a few locked files on my boot drive(s), but if you look at which ones they are, you can add them to an exclude file. In my case, they are all things that do not need to be backed up. If you do need to back something up, and can't exclude it, use an alternate boot system, as suggested earlier.
Log files (which should always be closed after writing, but usually aren't), usually don't need to be in a backup.
SWAPPER.DAT is recreated at each boot.
INI files, with the extension ".!!!" don't need to be backed up.
Files in %TEMP% don't need to be backed up (NEVER keep anything in the system temporary file folders).
If you think about it, there are probably other files, and folders, that don't need to be backed up.
You also need to be sure that nothing is open, if you need to back it up.
Okay, the parameters (the order doesn't matter):
-9 is maximum compression. It slows it down a bit, but makes a smaller backup file
-r is to recurse through sub directories
-y is to handle symlinks (VERY important on the %UNIXROOT% drive, but I always use it)
-S is to include hidden, and system, files (VERY important on boot drives, but I always use it)
The batch file, that I use, is:
if exist CDRIVE.ZIP DEL CDRIVE.ZIP
zip.exe -9yrS CDRIVE.ZIP C:\* -x@exclude.list 2>&1 | tee.exe CZIP.LOG
(change to match what you want to back up). The backup is made in the directory where the batch file runs, so exclude that from the backup. I put the backups on my HDD, (for speed), then copy them to alternate media (USB stick, network drive etc.), later. Exclude.list is a file with all of my excludes. I push the output through TEE.EXE, so I get a log file, and I can see what it is doing, at the same time.
I make a batch file, for each drive, then start them all at the same time. Each one goes slower than when run alone, but the overall elapsed time is less. YMMV.
Be sure to TEST your backup, to be sure that it actually does what you think it is doing. To do the UNZIP, I usually use the Archive Tool, as supplied by ArcaOS, AFTER doing a new FORMAT of the drive for a full restore, or just select the parts that you need. This does, of course, require an alternate OS/2 boot system, if the boot drive is involved (I always keep an alternate boot system available). To do the test, i recommend using a different HDD, so you can be sure that it actually works, before you need to depend on the backup. You can, of course, use the UNZIP command (under an OS/2 boot).
NOTE: ArcaOS uses the ZIP.EXE and UNZIP.EXE, that is supplied by RPM/YUM. That won't work, if you don't have the YUM stuff installed (for some reason). There is an older version of ZIP called ZIP2.EXE, in the C:\sys\install directory. It is limited to less than 2 GB files (in, or out), but your boot drive probably qualifies.