What can cause long query durations without high resource usage?

As you are running SQL 2005 you can take your SQL Profiler data and compare it against the Perfmon data to see if you can see a correlation. This is done by saving your trace data and perfmon data to files using the normal techniques. Then open the SQL Profiler trace within profiler, and then one of the options in the file menu will be Import Performance Data. This will let you select a query and see what the counters were doing at that time (or close to it depending on your perfmon collection interval).

Disk queue spikes are never good. Especially that high. What's the IO that you are pushing to the disk when the queue gets that high? Basically you don't want a disk queue any higher than (2*n) where n in the number of disks in the array. Since you are using a 2 disk RAID 1 n=1 in your case (since you only get the speed of a single disk).

In perfmon there's a counter which is the seconds per read and seconds per write. What do these counters look like when the queries start taking a long time to run. What about normally? (Anything over .02 seconds is bad.) What's the estimated page life expectancy? (Anything under 300 seconds is usually bad, but this can vary.) What's the SQL Server cache hit ratio? (Anything below ~97% is usually bad. I like mine above 99.9%.)

Few things that maybe unhelpful or could be useful;
If this is happening to stored procedures, it could be parameter sniffing -> http://omnibuzz-sql.blogspot.com/2006/11/parameter-sniffing-stored-procedures.html
Are you using ASP for the web application? We had an issue that was similar but related to ASP + IIS and SQL using stored procedures. I seem to remember it being semaphore timeouts that would cause this. It'd take almost 30+ seconds to run a query but then everything was fine for a while. I can't find my info on it but I seem to remember it being related to IIS timeouts, this was on the IIS side.

This tool might be helpful too -> http://blog.brianhartsock.com/2008/12/16/quick-and-dirty-sql-server-slow-query-log/