1. if you have Win x64, the more RAM, the better, I have 24GB and still get RAM full every now and then - http://blogs.adobe.com/toddkopriva/2009/12/performance-tip-dont-starve-yo.html or http://blogs.adobe.com/toddkopriva/2009/03/cs4-production-premium-on-64bi-1.html
2. generally yes, desktops are faster than laptops, and you have more possibilities to upgrade/extend your rig afterwards. Also, most laptops only have room for 1 HDD, and having all files on a single drive will decrease performance drastically.
3. That's not how this issue is adressed. You go the other way around: think of how much you can spend and build a rig around that.
4. - video card with OpenGL 2.0 or later (most newer cards have already 4.0) - pro graphics cards like Quadro generally perform better than gaming cards;
- separate HDD for media/projects (the faster the better); prefferably a 3rd HDD for renders;
- enough RAM (the more the better)
- fast CPU - check http://www.cpubenchmark.net/high_end_cpus.html and see what you can afford
5. additional reads:
- google performance tips in after effects
P.S. don't cheap out on the mobo, it's the central part of your comp. You get more performance and reliability with a good mobo + slower CPU than cheap mobo + monster CPU
If you really care about performance, and you're ready to spend a little money, I strongly recommend updating past After Effects CS4. After Effects CS4 is a 32-bit application, whereas After Effects CS5 and later are 64-bit applications. This makes a huge difference for performance.
I recommend going through the resources here:
You can easily spend 15000 or more for a high-end system, depending on what you are doing with it.
Generally, prices tend to explode as soon as you decide you need more than one cpu. Look into the specs of a HP Z800 or a MacPro. If you are capapble of building your own system, you can certainly save quite a bit of money; of course you are on your own regarding support.
As marian said, go for higher quality components instead of those with the highest benchmarking score. I'd also avoid overclocked stuff, expecially on the cpu side for AE, unless you know exactly what you are doing, have a spare available and no unreasonable deadlines looming ahead. Consider spending extra attention to cooling your rig. And you definitely would avoid to noisy components.
Having said all that - considering you started on a Laptop running CS4, you might find a decent Sandy Bridge motherboard running a i7-2700 CPU, at least 16GB memory and a couple of hard drives with a decent graphics card ( really anything at around 300) and upgrading to CS5.5 like the step into a new universe. This shouldn't cost more than perhaps 1200 and is, for starters, not too shabby.
If you need more, but not immediately, I'd recommend to wait until Intel gets its new Xeons ready with the corresponding motherboards.