I was wondering if some one could help me order the cipher suites in Server 2008 R2 from strongest to weakeast.

I did this in Server 2008 but I don't know about the new suites added in R2.

I have the following to choose from:

TLS_RSA_WITH_AES_128_CBC_SHA         
TLS_RSA_WITH_AES_256_CBC_SHA         
TLS_RSA_WITH_RC4_128_SHA           
TLS_RSA_WITH_3DES_EDE_CBC_SHA        
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA_P256   
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA_P384   
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA_P521   
TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA_P256   
TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA_P384    
TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA_P521
TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA_P256  
TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA_P384  
TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA_P521  
TLS_ECDHE_ECDSA_WITH_AES_256_CBC_SHA_P256  
TLS_ECDHE_ECDSA_WITH_AES_256_CBC_SHA_P384  
TLS_ECDHE_ECDSA_WITH_AES_256_CBC_SHA_P521  
TLS_DHE_DSS_WITH_AES_128_CBC_SHA       
TLS_DHE_DSS_WITH_AES_256_CBC_SHA       
TLS_DHE_DSS_WITH_3DES_EDE_CBC_SHA
TLS_RSA_WITH_RC4_128_MD5                    
SSL_CK_RC4_128_WITH_MD5           
SSL_CK_DES_192_EDE3_CBC_WITH_MD5       
TLS_RSA_WITH_NULL_SHA
TLS_RSA_WITH_NULL_MD5            

TLS 1.2 SHA256 and SHA384 cipher suites:

TLS_RSA_WITH_AES_128_CBC_SHA256
TLS_RSA_WITH_AES_256_CBC_SHA256
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA256_P256
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA256_P384
TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA256_P521
TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P256
TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P384
TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA384_P521
TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA256_P256
TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA256_P384
TLS_ECDHE_ECDSA_WITH_AES_128_CBC_SHA256_P521
TLS_ECDHE_ECDSA_WITH_AES_256_CBC_SHA384_P384
TLS_ECDHE_ECDSA_WITH_AES_256_CBC_SHA384_P521
TLS_DHE_DSS_WITH_AES_128_CBC_SHA256
TLS_DHE_DSS_WITH_AES_256_CBC_SHA256
TLS_RSA_WITH_NULL_SHA256

TLS 1.2 ECC GCM cipher suites:

TLS_ECDHE_ECDSA_WITH_AES_128_GCM_SHA256_P256
TLS_ECDHE_ECDSA_WITH_AES_128_GCM_SHA256_P384
TLS_ECDHE_ECDSA_WITH_AES_128_GCM_SHA256_P521
TLS_ECDHE_ECDSA_WITH_AES_256_GCM_SHA384_P384
TLS_ECDHE_ECDSA_WITH_AES_256_GCM_SHA384_P521

Without going through everything line by line it helps if you break down each cipher suite into three parts: the key exchange, the encryption, and message integrity and then make your preference decisions.  The larger the keys the more computationally intensive they become.

In the end, most of those are completely unbreakable so it doesn't matter what you choose.

All the key exchange asymmetric algorithms are incredibly strong so it really doesn't matter.  You can avoid the old ones by dropping these choices off the list because they are relatively weak as are their hashing and encryption:

SSL_CK_RC4_128_WITH_MD5      
SSL_CK_DES_192_EDE3_CBC_WITH_MD5  

These offer no encryption only message integrity so get rid of them as well:

TLS_RSA_WITH_NULL_SHA
TLS_RSA_WITH_NULL_MD5 

TLS_RSA_WITH_NULL_SHA256

Anything with AES is suitable for use.  The larger the key length the stronger it is.

SHA is a strong hash and even the smaller digest sizes are still acceptable and in common use.

Prefer TLS 1.2 for the most part but just remember that old browsers won't be able to negotiate the newer algorithms if you completely exclude the old ones.  I'd disable the ones that were part of the old SSL standard though since there are vulnerabilities IIRC.

I second what Matt W. wrote, but like to add a few things:

The FIPS Suite B protocols are in general more secure.

There is another thing: Perfect Forward Secerecy (PFS). You'll get this only with elliptic curve cryptography or Diffie-Hellman.

So my personal grouping is:
1. TLS_ECDHE_ECDSA_...
2. TLS_DHE_DSS_...
3. TLS_RSA_WITH_...  
4. SSL_...

Keep in mind though, that the other side (e.g. webserver) also determines which protocol is used. Due to higher performance impact, the Diffie-Hellman protocols are disabled on many webservers or not enabled by default (MS IIS).