If you're using DFS-R, which is included with Server 2003 R2, the Microsoft Directory Services Team has put together an excellent post explaining the top 10 reasons why replication may be slow.

In short, the top 10 are:

1. Missing Windows Server 2003 Network QFE Hotfixes or Service Pack 2
2. Missing DFSR Service's latest binary
3. Out-of-date Network Card and Storage drivers
4. DFSR Staging directory is too small for the amount of data being modified
5. Bandwidth Throttling or Schedule windows are too aggressive
6. Large amounts of sharing violations
7. RDC has been disabled over a WAN link.
8. Incompatible Anti-Virus software or other file system filter drivers
9. File Server Resource Manager (FSRM) configured with quotas/screens that block replication.
10. Un-staged or improperly pre-staged data leading to slow initial replication.

Along with each of the top ten problems are specific recommendations to assist with fixing the problem. A list of common tools used in troubleshooting and administering DFS-R is also provided. All-in-all an excellent list.

Check it out at: http://blogs.technet.com/askds/archive/2007/10/05/top-10-common-causes-of-slow-replication-with-dfsr.aspx