The "right" way to handle this is to actually reinstall and reconfigure everything - as you're trying to avoid.
DO NOT just copy everything from your old drive to the new drive in the manner you specify. If you do this, the best that will happen is you'll only be able to access 6 gigs on your 40 gig drive.
Depending on the services (and what versions they're at as opposed to the new versions you're going to install), you'll *probably* be able to just copy the configuration files over.
There's no such thing as an "ideal HD config for a server" because just about every server operates differently. Generally speaking, mount your drives with "noatime", format them to segregate writable and non-writable portions (an then mount those non-writable portions read only)
The more drives you have your system spread across, the better (to a point). The reason for this is simple, each drive head can only be in one position across all the platters at any given moment. This means that even if you have your system partitioned out correctly, you can only read or write to/from one partition at a time, whereas if you have two drives, they can both be operated on simultaneously. This is true whether you're using RAID or not.
More core (RAM) is always better than faster core. Even though DDR is faster than PC1xx, it's still about a hundred times slower than the processor. Once you're physical RAM space fills up, data that needs to be stored has to be written to the hard drive - which is what swap space is for. The more your system has to resort to the swap space, the slower it gets because that effectively slows the memory access times down to hard drive speeds which are about a hundred times slower than volitile core (RAM). So, on the issue of RAM, I'd take a 1gig PC133 system over a 512MB DDR system any day. Besides that, RAM is so cheap, I couldn't actually justify buying a 512MB chip anyway.
Since you're even asking the question of whether to use DDR or PC133, that means that you either have a k6 or k7 board (or thereabouts in Pentium numbers) that has the option of using both, or you're looking at upgrading your motherboard. If either of these is the case, throw that out (or relegate it to firewall duty) and get yourself something with a 64 bit processor. I say this mainly because you state that you're pushing web sites - which means you're probably using MySQL and Postgres, which both run better on 64 bit systems (because they both have native 64 bit code which has to be "translated" for 32 bit systems).
If you have the resources to do so, build a new system apart from the current server and make sure everything works the way it's supposed to, then just copy the web sites and databases over and have it take over for your current server. You're already talking about replacing the hard drive and RAM so you might as well just do the whole thing. You can usually build a decent 64 bit server from the ground up for less than $600 US these days (and you've already spent $200 of that).
my $.02
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