Ext3 is starting to get old as far as features and performance are concerned, but there is a one huge upside to maturity: stability. If you intend to keep the system around for a long time, or store important files on it, I'd go with ext3. I'm not saying that ext4 is unstable, I'm only saying that ext3 is really really freakishly stable ;)
If you're just a regular desktop user, it really doesn't matter, because caching will have WAY more impact on performance than any internal structures. The only big win for ext4 is when you're intending to store lots of large files, then you want to format your partition with ext4 with extents. Another big win for ext4 is if you're forced to store large (>32000) files per directory.