I try to keep the center and top clear of UI elements so you can see the action better.
Chat windows are at the bottom left and bottom right; chat windows at the top can block characters/faces during cut-scenes (I have the cut-scene dialogue in my chat boxes), so I have them moved to the bottom.
Hotbars are all moved to the bottom so if there are any that don't have hotkeys, they are all centralized (instead of having to click all the way on the left or right side of the screen). Also by having them in the center, you can easily see cooldowns.
Party and companion elements are a little closer to the middle for easier targeting. Health of Target is enabled as well.
Updated: Added 2 pics (UI layout and in-game)
Updated: Realized I left the companion cast bar under the left chat window. I moved this just over the companion toolbar and took 2 more screenshots to reflect this and to show the companion and companion toolbar in use.
Update 4-13-12: I adjusted my UI a little to make more sense for Naga users. Now the hotkeys match up better with the orientation of the Naga. It's 3 across by 4 down instead of 4 across by 3 down. I had to shift the Focus Target and Target of Target up just a little to accomodate this, and I also made the chat windows a little bit wider. I also adjusted the global scale back to 1 but shrank down some individual windows like the party windows. It's still a lot tighter and cleaner than the original UI, but now the hotbars are a little bigger than before (by .05) so it's easier to see (at least by my old eyes for global cooldowns or if you happen to be a clicker. Older versions should be archived.
Update: 4-16-12. I adjusted the UI scale of the mission tracker from 1.0 to 0.9 so it's taking up less space now. It's still easily legible, but less intrusive to the center of the screen, so it's a bit "tighter" now.
Update: 4-19-12. I moved the Ops frames up a little to avoid collision with chat frame. I also extended the height of the health bar in the Ops frame (for easier healing) and added Text to Ops, player, and target frames.
Update: 5-14-12. Minor update. I noticed the player window and target window were slightly off, so they were not symmetrical. I know this is very minor, but it was irritating me, so I adjusted it so that it should be very close to symmetrical now.
Update: 7-9-12. Minor update. I found the response wheel was too low, so it was blocked by the player and target portraits. I raised it up a little so it's completely visible again.
Update: 9-23-12. Minor update. I found when running FPs that the target window was too low, and the ToT window was interfering, so it made it difficult to see the difficulty of the mob (strong, elite, champion, etc). I adjusted the lower right chat window down slightly. I raised the Player and Target windows slightly, so now you can easily see the difficulty of the mob, and all of the shifts were minute.
Update: 9-23-12. Ok, I was just kidding about the last update. Now that I've moved the chat window lower on the right, I also lowered the companion bars to match it.
Update: 11-16-12. Update for release 1.5. Added 2 additional hotbars, one on each side. Moved the companion bar in to accommodate the right hotbar, and move the party and ops window on the left a little more in to accommodate the left hotbar. Left the Cartel icon in the default location. Realized my Combat Awareness indicator was slightly off center, so I adjusted this. Added 2 screenshots as well.
Update: 11/26/12. The "General" tab/window should be the main window, but it defaults to "Other" each time I log in (this has been occurring for a while now). I previously submitted a bug report about having a "default" window, and CS admitted this is a bug, but I suspect it is low priority for them. I went ahead and submitted another bug report to them today to see if they will escalate.
For my UI, I swapped the "General" chat window and the "Other" chat window so "Other" is on the left and "General" is on the right. As others have mentioned, the "Other" chat window becomes the default when you log in or load screens, so you have to set focus to the "General" window each time. This is a pain for many (myself included), so I decided to switch their positions. This means that you'll need to adjust which chat channels you want in each window/tab so they are opposite of what they are now.
Update: 11/27/12. Another user mentioned the Ops frames kept resetting, so I ran a few WZs to check it out. Sure enough, it gets pushed up after you load/zone. I don't know why this is happening, but I will /bug it in game. I don't do a lot of WZs or Ops, so I didn't notice this right away. I did make the Ops frames wider and shorter instead of tall and skinny so it's easier to click for healers and generally closer to the rest of the UI. I also moved the HuttBall score panel so it doesn't interfere with your mission tracker.
Update: 4/21/13. Adjusted the caster bars slightly up. If you have 2 rows of buffs, they were overlapping, and you can see a weird graphical bug during casting. Now that 2.0 is out with Achievements, I also moved the Achievements frame to the top left next to the map. Inverted it so that it's actionable component is at the top instead of the bottom.