data logging/processing

Are you logging when the transaction occurs, too?

No, I have no RTC or Arduino based timing at present

Capturing and showing it where? The Arduino does not have a lot of memory, so it will not be able to hold much data.

Eventually I would like data presented via web, but for now (testing) through the Serial Monitor would be fine

You could add an SD card, to increase the amount of data you can store.

I have bought a W5100 based Ethernet/SD card shield for later development, maybe I could use the SD card to store data now.

Showing that data may or may not be trivial. Depends on where and when you want to show it.

As mentioned, eventually to share formatted results/database queries over the internet. (reference Pachube/Cosm) I am just starting and didn't want to take too bigger steps, get the animals to trigger inputs (done), add direction and count "in"s and "out"s (done), present the data against time intervals on serial monitor...don't know here to start!

What would trigger showing this data? Per channel or an aggregate?

Eventually live streaming to web, but for now a selection of formatted results. "in"s in the last hour, total "in"s today, that sort of thing.

Collect it where? Retrieve a file from where?

At the moment I would like to just print running totals to the serial monitor but next step would be to push it to a file for Excel, then ultimately to present via web a range of live streamed results.

I would simply stuff each animal entry/exit event into a MySQL database, using an ethernet shield. The server hosting the database could timestamp the entries.

Then, use the power of SQL to extract the data that you want - entries and exits in the last hour, the last 24 hours, the busiest channel, etc.

I have no idea about SQL databases or Ethernet shields yet. I think I am after a generalised explanation of how you capture, manipulate and show data such as I am collecting. As an example, how would I deal with working out the total "in"s in the last hour as a rolling total?
Sorry for not asking very specific questions, but I only know what I am trying to achieve and not the tools or techniques I should use.
Cheers Simon