I find that H.264 is too CPU intensive and slow for scrubbing so I use the Apple ProRes codec, which thankfully is also quick to encode. The downside is that it produces a large filesize but it's pro's heavily outweigh the con.
But, I would not recommend using a compressed file format. With Terabyte hard drives going for $100.00 or so, storage costs pertaining to large files are not too harsh. You'll get the best results using uncompressed files so the computer CPU isn't burning up cycles uncompressing the video when it could use it on some CPU-pig plug-in of your choice. Better results are also achieved streaming the video from a separate hard drive on its own bus.