It's about future expansion, mainly. Put in 2x1GB now, and you can expand with another 2x1GB, limiting you to 4GB. Put in 2x2GB now, and you have the option to put in another 2x2GB later. It's about not having to toss out those 4 1GB sticks if you ever want more than 4GB total.
Also, only having 2 sticks instead of 4 puts less strain on the system. I'd recommend only using half the memory slots of a motherboard for any gaming PC, if only for that little bit lower power-consumption and slightly (unnoticeable) increased stability+performance.
That post you linked to has another good point: more memory makes it less likely to run out, which avoides paging to the HD (though more than 4GB is never nescesary with current Windows versions; any single program is limited to 2GB max). I ran 2GB for a while, but went to 4GB eventually (from 2x1GB to 2x2GB). Can't say I really notice the difference, but at least I know that if a game needs the full 2GB it can ask for, it's available with plenty to spare for the OS and other progs running in the background.
Imho, considering the prices, there's really no reason to not go for the 4GB. You'll never regret it, I can promiss you that.
For the 64 vs 32 bit thing, I'd say go with 64. I only switched to 64 bit when the Win7 beta came around, and I haven't run into any issues yet. All I had to do was collect the correct drivers for my system, that's it. Don't know about this "emulation mode", but if it's there it's fully transparant; no actions are required from you to get something running.
Win7 (and I guess Vista) puts 32bit apps in a different "program files" folder as 64bit ones. I guess as long as you stick with the default directories there's nothing to worry about. Though I put all my games somewhere else (all 32bit, offcourse), and everything runs fine.
*ah yes, and you gain excess to the full 4GB of RAM, should you go with that.