I would get Intel Q35 for Intel CPU setup or AMD 780G/790GX for AMD CPU setup.
They both as integrated GFX:
Intel Q35 --> with Intel open source drivers will work almost everywhere.
780G/790GX --> most powerful integrated card ever (HD3200/HD3300) open source drivers currently do @d (RadeonHD) but 3D will come in some time (1 year?).
Also Intel Q35 has Intel VT-d extensions.
Nvidia also should work, but only i386 and only binary driver.
AMD also has several very interesting small power consumption CPUs:
Athlon X2 3400e (22W) 2x1.5GHz
Athlon 64 X2 3800+ EE (35W) 2x2.0GHz
Athlon X2 BE-2400 (45W) 2x2.3GHz
Athlon X2 4450B (45W) 2x2.3GHz
Athlon X2 5050e (45W) 2x2.6GHz
As for Phnemons, there is 'e' series that is very power efficent:
Phenom X4 9350e (65W) 2x2000 MHz
Phenom X3 8450e (65W) 2x2100 MHz
AMD does CPU 'better by desing' but Intel currently wins because of 45nm process High-K Metal Gate design. AMD still uses 65nm SOI which is slower, but AMD CPUs has better features, like Nested Page Tables, Integrated Memory Controller, Tagged TLB. You will find none of these in Intel CPUs, at least till intel Nehalem will engage.
For example Intel Quad Core is nothing more then two Dual Cores stick together, and Each core does not communicate with other cores in CPU , but by North Bridge of the motherboard, its like using an email to talk to a friend that is sitting just above you.
Imho Intel e6320/e6420 (65nm) are good for everything, has virtualization and is cheap, anything newer/faster then that is ok. If you want 45nm CPU (cooler / faster / less power consumption) then go for e8xxx series.
About benchmarks, it depends what you measure, Intel is definitely better for games, but for servers AMD does really good:
http://it.anandtech.com/weblog/showpost.aspx?i=443
http://it.anandtech.com/weblog/showpost.aspx?i=467
http://it.anandtech.com/IT/showdoc.aspx?i=3335&p=6
http://it.anandtech.com/IT/showdoc.aspx?i=3335&p=7
http://it.anandtech.com/IT/showdoc.aspx?i=3335&p=10
You may also wait for AMD's 45nm CPUs
Daneb and
Shanghai which will be avialable at the end of current year.
You can go for standart 800MHz DDR2 5-5-5-15 or get some faster ones like 800MHz with 4-4-4-12 or 1066 with 5-5-5-15, but the difference is very, very small. 2 x 1GB is more then enought.
In short some modern 7.200RPM SATA2 drive, if you got too much money you can get SATA2 VelociRaptor 10.000RPM drive.
Get some good brand, like Chieftec/Thermaltake/Zalman/Antec/Be-quiet/Tagan.