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Well, it depends on how big the screen is that your project will be displayed on.
Basically you want to make it a size that will be displayed fully on screen taking into account the menu bars and borders of the Browser (like the dreaded IE6), plus the skin and playback controls of your actual project.
Any resizing you have to do does degrade the quality of the project.
With that said, when I record some software demo's, I maximise the software, and record the whole screen. Then I resize down to 1025 x 820.
But that's just me.
I use 1000 x 680 as my maximum finished size*, so it will play (without scrolling) in a browser with system resolution set at 1024 x 768.
Used to be that 1024 x 768 was the highest setting for some laptops. Now I assume that because many of my end users are in the 'bifocal' stage of their lives, they don't set their system resolution much higher than 1024 x 768.
If you're publishing to be played in Flash player, you can go to higher dimensions.
I suggest a dry-run capture/publish and then a test by a few real-world end users. Then decide.
* BTW, for most of my projects, I capture at 1000 x 620 and resize to 1000 x 680 so I can add a 30-pixel graphical header (with room for text and the Captivate drop menu) and 30-pixel graphical footer, (with room for text and the playback controls.