This seems to be a pretty common problem for Cisco users. Not that Cisco devices have more queue drop problems, just that more Cisco users are a little confused by the information generated in the show interface command.

Specifically, we're talking about the lines that look something like this:

Input queue: 0/75/0/0 (size/max/drops/flushes); Total output drops: 0
Output queue: 0/1000/64/0 (size/max total/threshold/drops)

Output queue drops are usually pretty easy since they are indicative of congestion on the network link. Input queue drops are more subtle and related to how incoming traffic is routed. There are two documents that can really help you solve and address queue drop issues.

• Troubleshooting Input Queue Drops and Output Queue Drops
  This document is full of lots of juicy details. In addition to describing the situations I mentioned above, it gives you various commands you can run to figure out what exactly is causing the problem.
• Performance Tuning Basics
  This is a very basic document that will likely only help you in the most general way. It describes the various switching paths and how they affect router performance. If you're using <acronym title="Cisco Express Forwarding">CEF</acronym> you are probably doing it right.