As great as Ubuntu is, it's not completely self-healing - especially after almost a year of dicking around with it on my desktop. So I finally decided two days ago to start from scratch again as there were too many little things that weren't working for some reason or another. It's *much* nicer now.
At first, I was thinking about doing a complete "clean install" as I've upgraded this box a couple times so far as new distribs of Ubuntu were released. I started on Edgy, went through Feisty and am currently running Gutsy and may move to the Hardy alpha once it gets a bit more stable. But then I thought that most of my problems are probably just from the insane amount of geeking and tweaking I've done in past year with tons of stuff gunking up my home directory. The number of hidden "dot" files in /home/russell was insane.
So I simply renamed (mv'ed) my home directory, re-created it, re-logged back in and got a fresh and shiny new desktop. Wallah! Things are working muuuuuch better now! For example, Compiz was giving me trouble before, now it's fading/zooming/shimmering beautifully. I love the virtual workspace sliding feature - it gives a real visual feel to where your other workspace is. Also, the various tweaks that I made to the GConf settings have returned to where they were before... and now that I have a better idea of what I'm doing, I'm pretty much leaving most things as they are. There's a lot of stuff I originally changed just for change's sake that ended up making the whole desktop crufty.
I went into my old home dir and copied over some of the things I didn't want to lose, like my .fonts dir and PGP key files, .ssh settings, etc. But I made a specific choice to start using Firefox from scratch rather than just copying over the mozilla settings dir. I imported my bookmarks, but that's it, everything else is brand new and added manually - like the various plugins, passwords, etc. Much cleaner... but now for some reason my tabs aren't being saved automatically... I'll have to figure out what I did before to make that happen.
Anyways, if you're on a Linux/Unix box, I definitely recommend doing something similar if it's been a while... it's like getting a whole new desktop.