Your going to want to put most of the focus on IO for a mySQL server RAM/HDDs/Network, you generally want a seperate machine optimized for each task you need done. If your planning on running a single machine than your server needs to be built for virtualization. It's also a lot easier to design the hardware since your going for all computing power, you will also be utilizing the entire system if you implement it correctly.
I came up with this list of hardware for virtualizing a web server, mySQL server, and application server. I assume you will be running linux as the OS and reusing network cards from the old server.
You won't actually need or really want a video card in your system, the board I suggested in the list below comes with integrated graphics built onto the board. Also the velociraptors are not the wisest choice for a server chasis, due to heat/ fail rate. Stick with SAS drives if your going 10k or higher RPM.
Motherboard -> $421 SuperMicro X9DRW-3F - integrated graphics, 2p for optimal virtualization allows installation of up to 512GB of registered ram, and has 6 sata ports and 8 SAS ports onboard SAS is capable of raid 5
CPU -> $1268 -> $634 per CPU x 2 = $1268 xeon e5-2630 -> support everything needed
RAM -> $520 64GB 8X16GB RAM Memory for SuperMicro X9 Series 1333 MHz -> 4GB for the host 32GB for the
HDDS -> $170 x 4 = 680 SAS CHEETAH 15k 450GB 4 would b to make a raid 5 array when micron m500 980GB ssds become available I would recommend using 3 for a secondary raid 5 array to handle the bulk of IO these will still be good for sequential writes but you will need to configure the OS to handle this
SSD -> $490 Intel 320 Series 300 GB -> for the host system boot drive, can be partitioned for SSD caching, and VM OSes
CHASSIS -> $426 SuperChassis 113TQ-600W -> PSU included
COOLER -> $70 -> $35 per cooler x 2 dynatron 1u active cooler
TOTAL $3995
If you can put up more details on about your current setup and what the intent of the build is and the level of use of your current build it would be easier to suggest an effective longterm build this time.