Using rsync to backup

For Maximum Safety, Copy Everything

The safest option is to copy everything, including invisible meta-data files.

Files tend to exist for a reason and as software changes, so will the existence, purpose, and contents of these meta-data files. Copying everything will reduce the maintenance burden and offer ease of mind that nothing is being lost.

The log file created by rsync will be technically involved by the very nature of rsync being a command line tool. Consider presenting a tidied up, meta-data filtered, and maybe even coloured coded output for the user to check. You could do this with a wide range of scripting tools and languages. Please ask more questions here on Ask Different and on StackOverflow if you need help with this approach.

Delete Last & Copy OS X Resources

Regarding the rsync flags, take a look at the question Fastest and safest way to copy massive data from one external drive to another. In this question, a few additional flags are used and explained:

sudo rsync -vaE --progress --delete-after /Volumes/SourceName /Volumes/DestinationName

In this situation, the E will ensure resource forks and other Mac specific properties are copied.

You may want to consider --delete-after to avoid deleting until the copy has completed; please note that this approach will potentially require a destination drive twice the size of the source.

Possible Exclusions

An answer to a related question, How can I omit FCPX Render Files from a Time Machine backup?, provided a useful link of OS X files and folders that can be excluded from most back-ups. This link provides a practical list of file patterns, folders, and paths that you could exclude.

Include dot Files

There are good reasons to back up files beginning with dots, .* matching files.

Some software keeps preferences, settings, and other information of value in folders at the top of the user's folder in invisible dot prefixed folders. Running ls -la ~/ will reveal these folders and files.

If any user uses or has software that in turn uses version control software, be sure to back-up dot files. Software like subversion and git both store critical information within their dot folders. These hidden folders can be scattered across your file system, where ever a project is checked out.

Spotlight and Disk Access

Spotlight is OS X's search service. Spotlight uses the mdworker process to index and update the search catalogue. If you are concerned about possible disk corruption or slow copies, disabling mdworker while running rsync may help. Personally, I leave Spotlight running while running large rsync transfers.

I'm not completely pleased with the current answers, but I will try to cover here a bit of the possibilities that I've seen on the web trying to find a nice setup for rsync.

And, by the way, if one is interested in Time Machine like copies, there's rsnapshot. And there's also Unison for two way syncronizations. Plus, there's actually a few GUIs, like Backup Utility and arRsync; not exactly what I was looking for but they might do the job for somebody.

First, my only intention was to duplicate photos and videos, so exact copy wasn't needed, hence no need to care too much. In fact most of my doubts were if I could exclude everything (the same that would happen if, say, I downloaded a photo from the internet, I just download a .png, everything else is not downloaded but autogenerated).

Here's an unstructured list of thoughts that you may want to take in account

I you want to ensure that your laptop doesn't go to sleep, you may want to caffeinate the process caffeinate -s rsync -av .... Taken from here.
If you are doing local copies, like in my case, or even if internet connection is not too slow, you should not use -z option (compression), and use -W (transfer whole file, rather than delta transfers; this is a default when local) and probably use --inplace to make transfers fast. Taken from here.
You can use --delete-after so any file will be first transferred, and then moved on destination (and deleted the original one) and is safer than deleting before the transfer or during the transfer.
You can stop the transfer by pressing ctrl + C, and it will stop cleanly. Taken from here. This was one of my fears with SuperDuper!, if you need to stop a transfer you get the message “You will leave the hard drive in an unknown state…”.
In recent versions there's --info=progress2 which adds even more details to -v.
There's -P (which equals --partial and --progress) that will leave mid-transferred files there so you can keep going when you restart the process (if for some reason you can't end the syncronization at once).
One might be interested in stopping Spotlight or TimeMachine before doing the copy, and reenable them after the transfer. And even disable Spotlight for the external disk.
Other options used in all those references include -x (or --one-file-system), -E (--executability), -H (--hard-links), -X (--xattrs), -A (--acls), and --sparse, --hfs-compression, --protect-decmpfs. You may want to look at them.

For me, a basic command looks like (I might use more options, but this is enough for an example):

caffeinate -s rsync -av --delete-after --progress --stats --exclude-from 'excludefile.txt' \
  "/Volumes/SrcHDD/" "/Volumes/DstHDD" # note the trailing slash / after the source

Now in my case I could just include {*.jpg,*.png,*.mp4,*.txt,*.pdf,…} and no one would say “you need also system files” but since I don't want to search to get all the possible filetype I have files of, I prefer to exclude. And there are things that not only can be but seem convenient to exclude.

I found a few links, take what you want:

https://bombich.com/kb/ccc4/some-files-and-folders-are-automatically-excluded-from-backup-task
https://gist.github.com/tvwerkhoven/4541989
https://github.com/necolas/dotfiles
https://gist.github.com/shkm/5531679
http://www.hackurmac.com/2014/08/backing-up-and-restoring-your-hackintosh.html
https://github.com/jedda/Counterpart
http://alanwsmith.com/rsync-exclude-list-for-mac-osx

And from there you could probably get what's safe or sane to ignore. Here's the full list (I just removed duplicates)

.HFS+ Private Directory Data*
/.journal
/.journal_info_block
.AppleDouble
.AppleDB
/lost+found

.metadata_never_index
.metadata_never_index_unless_rootfs
/.com.apple.timemachine.donotpresent
.VolumeIcon.icns
/System/Library/CoreServices/.disk_label*
/TheVolumeSettingsFolder

.DocumentRevisions-V100*
.Spotlight-V100
/.fseventsd
/.hotfiles.btree
/private/var/db/systemstats

/private/var/db/dyld/dyld_*
/System/Library/Caches/com.apple.bootstamps/*
/System/Library/Caches/com.apple.corestorage/*
/System/Library/Caches/com.apple.kext.caches/*

/.com.apple.NetBootX

/Volumes/*
/dev/*
/automount/*
/Network/*
/.vol/*
/net

/private/var/folders/zz/*
/private/var/vm/*
/private/tmp/*
/cores/*

.Trash
.Trashes

/Backups.backupdb
/.MobileBackups
/.MobileBackups.trash
/.MobileBackups.trash

Library/Mobile Documents.*
.webtmp

/Library/Caches/CrashPlan
/PGPWDE01
/PGPWDE02
/.bzvol
/Library/Application Support/Comodo/AntiVirus/Quarantine
/private/var/spool/qmaster
$Recycle.Bin
Saved Application State
Library/Preferences/ByHost/com.apple.loginwindow*

.AppleDesktop
.com.apple.timemachine.supported
Network Trash Folder
/Library/Caches/*
/private/var/spool/postfix/*
$RECYCLE.BIN
/stuff/*
/afs/*
/private/var/run/*
/Previous Systems.localized
/tmp/*
.dbfseventsd
.DS_Store
.PKInstallSandboxManager
.SymAV*
.symSchedScanLockxz
.TemporaryItems
Desktop DB
Desktop DF
hiberfil.sys
pagefile.sys
Recycled
RECYCLER
System Volume Information
Temporary Items
Thumbs.db
AUTORUN.INF
Autorun.inf
autorun.inf

If you're using rsync version 3.0.6 as per Carbon Copy Cloner or 3.1.2 as per Homebrew, you can take a cue from Carbon Copy Cloner arguments:

rsync -A -X -H -p --fileflags --force-change -l -N -rtx --protect-decmpfs --numeric-ids -go --delete-during --backup --backup-dir=</PATH/TO/STICK/BACKUP_when_using_delete> --protect-args <SRC>/ <DEST>