the best thing to do is use colums to purify that

lots of products out there

e.g.:

http://www.clontech.com/products/detail.asp?tabno=2&product_id=10560

http://www.stratagene.com/products/displayProduct.aspx?pid=394

http://www1.qiagen.com/Products/DnaCleanup/GelPcrSiCleanupSystems/QIAquickPCRPurificationKit.aspx

since you are using the gateway system, money cannot be an issue, can it?

I agree with vanishing: stay away from phenol extraction. I've used gateway a lot and standard pcr spin columns are usually sufficient. If your gels show contaminating PCR bands it is probably better to gel purify (again, use a qiagen kit or similar).
The annoying thing about gateway is the huge size of the primer tags, which makes spin columns less efficient in removing primer oligos and/or primer dimers. However, As long as these are not visible on a gel after purification you should be alright.

We've now switched to in-fusion cloning though, much better and cheaper.