The server is running Apache, Subversion, and Atlassian Confluence. Can this be upgraded safely, and if so, what is the command line? I'd like to stay on a more recent version of the platform but make as few problems for myself as possible.
According to Upgrading to Ubuntu 9.04:
Network Upgrade for Ubuntu Servers (Recommended)
Install update-manager-core if it is not already installed:
sudo apt-get install update-manager-core
Launch the upgrade tool:
Follow the on-screen instructions.
According to the Ubuntu release history, 8.10 will be officially supported for another year (almost). 9.04 is less than two weeks old so I'd perhaps be slightly hesitant to upgrade immediately unless you have a pressing need. If what you have now works just stick with it until the 9.04 issues are bedded down.
I would stick with 8.10 like cletus said. There aren't to many major differences between the releases. If you stick with 8.10 then you know what your getting, if you upgrade to 9.04 there could be bugs that haven't been reported yet that might affect you.
The major thing you have to consider when upgrading is this: Who are you working for? If this is your server then do it and see what happens. If this is a business server that servers the needs of other users, then wait.
If there's one thing vista taught us, it's that the "latest and greatest" isn't always better then what you were using before.
There is an annoying bug with tracker in 9.04.
Otherwise I haven´t seen any problems after upgrade from 8.10 after using it for couple of hours. Nor I have seen any significant differences or improvements. Upgrade itself went smoohtly.
EDIT: these experiences refer only to desktop usage, they are probably not applicaple to the question.
As cletus said, just do:
sudo apt-get install-update-manager-core sudo do-release-upgrade
However, I have usually found that upgrading can cause lots of problems. On desktops I usually put the home folders on a separate partition so I can do a fresh install without losing any data. If you don't have a really important reason to upgrade, don't. Upgrading is good for desktops so you can get all the cool new stuff. On servers though, you don't want to mess with more than you have to.
There's a bug in 9.04 where degraded RAID arrays don't automatically start. Otherwise, I've been happy with it on my home server and my VPS, but I haven't finished my testing for my work cluster(s) yet.
The only way you can really be sure is to upgrade the preproduction server and see what breaks. If you don't have one, then you can always restore from backups if you encounter something major and unfixable. If you don't have backups, well, may God have mercy.
Technically you can, see the other answers for how.
The problem I had with ubuntu upgrades, is every time I upgraded in the first month or so after a release a lot of stuff were broken, and it took some time until they were fixed. Good it is only on my home stuff.
I'd like to upgrade my servers as well, but I'd wait at least until the end of June before doing so.