well, i'm no expert, but you really want to go with a direct VGA input if you're going to be using a computer as the input. otherwise you're going to be converting from a VGA signal to an NTSC signal and the image you'll end up with will be much, much less clear. so, if you're going to be using the display for XBOX, or DVD but not a computer, then go for it. otherwise I'd really think you'd want to go for a display that accepts VGA natively. of course those are much more expensive than a pure NTSC/PAL display.
I just put a display in my car, in the double DIN space where the stereo would otherwise go, and I must say it wasn't all that hard to do. i've heard people make strong arguments against the motorized units. at first i wanted to go with one of those, because it would be so much easier to install (than trying to put one in the dash).
some people pointed out that the pop-out displays are a little awkward when it comes to pressing the touch screen, since they tend to move or shift as you press them. since they are not permanently affixed. i haven't used a pop-out one, so i can't say if that's true, but it made sense. also, a pop-out style can attract more attention when in use, it's clear it's not a factory installed nav unit, for example. i was a bit concerned about having a police car stop next to me at a light, see a pop-out display and decide that I shouldn't be using that. the law isn't on our side in these matters. by having it built into the dash i "feel" it's more likely to be mistaken or interpretted as a factory built in nav unit. as for thieves, well, i would think i am mildly more secure, which is only to say that while it's visible (versus a pop-out), you'd have to ruin it to get it out, so "perhaps" i'm less likely to be robbed (perhaps more so... who knows...)
the one major thing i would say against the in dash thing is glare. glare sucks. in bright light the light coming in through any/all of the windows is enough to make reading the display tough. i've heard that those pop-out display which can be angled (such as the one at digitalww) are useful for turning the display just enough to avoid some glare.
anyway... that's just my $0.02.