It will handle the currently available HDDs, like 3TBs without any issues. You may want to consider installing Windows and other programs on a smaller HDD like 320 GB to 500 GB (I have 500 GB), then utilize the larger 3 TB HDD for data storage, music, videos, etc.
In addition to the above, you must consider having an external HDD, 3 TBs as the case may be, for backups.
Mechanical HDDs are only pushing 120-150MB/sec, barely hitting SATA-1's performance ceiling. SATA-2 is not going to be a limiting factor on those any time soon.
The main benefits of SATA-3 are for either:
- high-performance SSDs
- SATA port replicator (large storage arrays)
For most people, SATA-3 is only needed for SSDs where the better ones can push over 500MB/s.