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Distribution: SUSE 9.1 Pro and Debian Testing on Server
I personally tend to prefer reiserfs for my root partition and ext3 for my home...and the reason for this is say i decide to switch to fedora, it doesnt have good support for reiserfs, so i format my root as ext3 and my home is already ext3. The only distro not capable of being installed on ext3 that I can think of off hand is Linspire.
Ext3 and Reiserfs are the ones to consider. I use Reiserfs myself and it's quite stable, but I've heard that if it gets messed up, it goes down hard. It also excels at handling small files, which *nix systems generally have lots of. Don't worry, it does well with large files also.
Ext3 is a journaled extension of the older non-journaled Ext2, which Linux systems used to use. It's therefore a bit more mature, has a bit better support, and is backwards compatible with Ext2 if you need it. It's a solid file system very good for general use.
So, really, the choice is up to you. They're both good choices. There are others, like JFS and XFS, but unless you have special needs, I wouldn't bother with them. I'd say just keep your Reiserfs unless you have any real need to change.
"For those of you still reading, congrats! The conclusion is obvious by the "Total Time For All Benchmarks Test." The best journaling file system to choose based upon these results would be: JFS, ReiserFS or XFS depending on your needs and what types of files you are dealing with. I was quite surprised how slow ext3 was overall, as many distributions use this file system as their default file system. Overall, one should choose the best file system based upon the properties of the files they are dealing with for the best performance possible!"
For a desktop system the filesystem speed is almost entirely irrelevant. It matters on a server because you may have dozens of users opening and closing hundreds of files at a time, but for a single user on a desktop...I wouldn't worry about it.