There are several things i would like to comment on:
I would pretty much stop at the CM Stacker. IMO, the CM Stacker is superior to the V2000 Lian Li because of the ease of wire management. We dont need a doll house of a case and the CM stacker provides all the things the V2000 provides such as dual power supply and a crapload of HDD slots and more, which means it also provides a conversion to BTX. Ive also studied each case in detail because i was tossing up between the two to convert to and the CM stacker came out on top because it's also easier to route watercooling through without extensive modifications to the case.
I would also like you to add the Antec SuperLanboy to the list for the budget buyer and also the lanner. The Antec SuperLanboy is seriously light, is a pleasure to install a system into (personal experience) and provides pretty much every feature that you might possibly need and has a carrying strap as well, all for $70 on newegg.
I would actually reccomend the 3200+ Winchester cored A64 for the budget buyer It's more than enough for anything you throw at it nowadays and OCs very well. The extra price to step up to the 3500+ just isnt justified to me.
For the CPU cooling, an A64 has several options open to it. Your heatsink suggestion is certainly a very valid cooling option. Very good cooling/noise ratio but not the best performer out there.
The Thermalright XP-90 and XP-120 are the best Air cooling AMD 64 options available (each one suited to different applications), coupled with an appropriate fan. The Zalman 7700 series coolers (a 120mm fan version of yours) is also a valid contender
It's tried and proven that A64's perform best with low latency memory instead of high speed memory. The absolute best memory for an A64 right now isnt the new memory sticks that came out. It's actually the old ram sticks with Winbond BH-5 chips. (Winbond stopped producing these somewhere around the middle of 2003) These memory sticks outperformed anything out there, putting out 2-2-2-5 at DDR400 without any problems at the default voltages and if you overvolt to 3v+ ive heard numbers going up to 250MHz (DDR500) at 2-2-2-5 completely stable and used 24/7 for 3 months straight (not sure after that as that was how many month's the writer has been using it for so far).
The best sticks would either be the Corsair XMS3500C2 sticks, Mushkin Black Level II or the Kingston HyperX KHX3200A, in their 256MB sticks or 512MB sticks. Coupled with either a voltmod or a OCZ Voltage booster, you should be able to OC pretty far on 2-2-2-5 with the A64 chip.
But due to availability problems, these BH-5 sticks are incredibly rare to find. But recently, Samsung introduced a new IC chip rated for PC4000 or DDR500 use dubbed the TCCD chips. Apparently, these run DDR400 at 2-2-2-5 without a problem and keeping these timings to somewhere between 210MHz and 220MHz. But the sticks with looser timings can reach up to DDR500 and beyond without a problem. Currently, these are the best RAM IC chips to be used in memory with an A64 system.
Currently, the best insurrection of the Samsung TCCD chips after a TCCD shootout on Anandtech is the OCZ PC3200 EL Platinum Revision.2 ram sticks. They also seem to not be suffering from any distribution problems and are in stock in newegg.
5. Hard Drives:
All the suggestions you made there are very good suggestions. I would just like to add some IDE based drives. The Western Digital JB line is also very good, dependable IDE drives that comes with a 5yr warrenty now. I have 2 myself and I've built countless PCs for friends/relatives with these drives installed and not a hitch on a single one. They've also got pretty good benchmark scores for drives of their class.
I prefer the Loigitech MX1000 laser mouse and a wired Microsoft Multimedia keyboard to the MX Duo, but this is my personal opinion after having used both systems for a while (Not the MX1000 mouse, but from having used one for 5 minutes at a friend's house it's good enough to win me over, but i already have an MX700 so i cant justify buying one for myself yet). The Multimedia Keyboard is more springy and provides more useful features than the Logitech one as well as being wired and can press more buttons all at once while registering than the Logitech. But this is all personal preference, different people prefer different keyboard/mouse combinations. But both suggestions are great combos.
Ive spent lots of time researching speakers in the 2.1 range and in that price range and ive heard quite a few speakers (I think i would have heard at least 60+ 2.1 computer speaker combinations) and in the end, i would think the Altec Lansing ATP3 takes the cake. It has amazing bass as well as an accurate treble (dunno how to describe this in English). It blows most of the speakers in it's class out of the water easily. Actually i havent heard those Kipslich speakers yet since they dont seem to be available in Hong Kong, but i would reccomend the ATP3 over anything else.
The rest of your guide is great. Good work there.