once the 100Mb/s link device's buffer is full, you'll end up in a fall-back situation, where you stop sending data to the device until your previous packets are acknowledged (at least, that's how it's supposed to work with TCP. With UDP, the application developer has to handle that themselves). so you'll have very few packets that overflow, if any.
they were probably saturating their uplinks. without QoS enabled, it's really obvious when a (relatively) low priority transfer is stepping on a service that needs higher priority, like VOIP.
in a small environment, I prefer to skip QoS configurations beyond voice (if you even want to bother doing that one), and make sure all uplinks are a bandwidth class above the switchports. so a 48 port gigE switch gets 10G uplinks. now no single user is logically capable of saturating an uplink. my last place had redundant network cores, so each switch got two 10Gig uplinks. each connection would be auto-assigned to the "other" uplink, giving you more bandwidth than having just a failover link.
