Since Ubuntu 9.10(karmic) have some issue with my external hard disk. I stopped and wait until 10.04 release. Here is how I update from 9.04 to 10.04 using clean install.
1), change the /home from ext3 to ext4.
2), format the root(/) to fat32 (using GParted in the Ubuntu Desktop version).
3), format the root(/) to ext4 (using GParted in the Ubuntu Desktop version).
4), install Ubuntu 10.04.
5), when install, choose where the root is install, and also set your /home partition as /home. (It will not format the /home, just for mount issue when startup.)
Note that on the step 2 and 3, it seems that it could directly format to ext4, or when install 10.04, it will format directly. But as I tested on other disk, It did not success, and it shows that it cannot remove another operating system (that is, 9.04). So I format the root to fat32, and than format back. Another reason is that if you delete the partition and create a new partition, the partitioning table on the harddrive may not work as what you expected. It may change from sda5 to sda9 (in my case).