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(We are using IIS and W3 extended format for logging)
Microsoft has a free product called LogParser. It is exceptionally fast at reading and rewriting log files. It can process a 100 MB log file in less than 30 seconds. You can parse the URL to be combined, use regular expressions to rewrite them, or run SQL-like commands against the whole log.
If you're using Clicktracks, you could pre-process your logs to rewrite your URLs in any way you'd like, or strip out any users, whatever. Then, analyze the resulting logs in Clicktracks, and take advantage of the lovely user interface.