You really should be getting something like this from a company like dell,sun, or ibm. Building it shouldn't be an option if this is a mission critical server. When something goes down do you really want to have it on your head? Or just say, yea its down, but we have same day on site support with sun and they will be here in an hour with a replacement part. I find that much better then "Yea, I ordered the new motherboard on newegg, it should be here tomarrow".
But again thats just me.
As for specs, I would need a better idea of the load that is going to be on the box. How many users? etc? Size of database? Type of database? How fast do you plan to grow?
This is something that if you dont know how to do already, you should be consulting with a professional. Unless of course this is just for a dev server, or a low load website for a small company. Then by all means have fun and learn They will be more understanding, and it wont cost you your job.
Then again (rambling) maybe your problem really isnt' you need a new server. Maybe you need to look at how your database is being used. What procedures and functions are being called, is your SQL standardized (everyone using the same caps, for example select * from table1 and SELECT * from table1 are too different querys to oracle, where if they were both the same it would pull from cache) Maybe you need to change your index's or use your indexs. Maybe you are doing crazy joins, or no joins. Maybe some of the work could be moved to the SQL server, or maybe the other way around, maybe some work could be moved to the webserver?
The trick is to find out what the weakest link is and how to improve it. Is it memory? Bandwith? Poor design? Building a better box is great, but what happens when thats full if your design is lackng? The final thing to think about is how this solution scales. Do you want to replace this server with a bigger one in a year? Depending on how fast you grow you may need something that is easier to scale. Maybe a blade, maybe just a rack that you can add a new box too and mirror. Maybe your storage requirements are growing and you need a SAN.
Ok enough rambling. Sorry