Yeah, Youtube does not need the black bars on the side for HD. This was an old necessity, and you can safely have a video at 960x720, and it displays very well. Even better for those of us who do not use a widescreen monitor (like me) because it isn't all squished in the middle. I encode all of my videos without bars.
Interesting thing about the lossless RGB though. When I have it checked, Fraps actually performs worse, most of the time. Though this computer sucks anyway so whatever. I can mess around with it more.
And as for 30 fps recordings, yeah, it's definitely better to do it this way. There's only one problem. Some stages of the Touhou games (namely, entering EoSD Patchouli fight) will re-lock the fps in-game to 30, even if using vsync. (pressing Ctrl does nothing) I don't have Fraps set to lock the fps, so I don't really know why this happens, so I have to use 60 fps in some areas. Just keep a note of that if that ever happens to you.
And as for me, I've reverted from using both VirtualDub and MeGUI, and just handle videos with VirtualDub, encoding them with H.264, resizing, and sharpening them. A scale of 5 for sharpening has so far looked good. Too high makes the video look bad. I'm still experimenting with it, but it looks to handle it better than MeGUI does. Still using Lame for the audio, just like MeGUI, just I pick CBR of 192. (because ABR of 192 does not exist) Also, media players seem to handle this format better than handling an mp4, and these finished videos are still in avi format. Not sure whether it makes a difference, but it definitely is easier to work with for me.