It is definitely a good idea to combine small outputs into larger ones, otherwise it is impossible to ever make payments in larger amounts (the transactions will be too big). Now if you only ever make small payments then I guess keeping the original small outputs is fine. But for larger payments they won't work at all, or will be too large to allow mixing. As far as mixin count to use when doing that, I can't give a good answer, as I haven't looked at the issues that carefully. The tradeoff is how many of these small outputs you can combine in one go. If you can't combine enough, you may need to do multiple steps.
The size of each transaction is dependent only on its immediate sources, not prior transactions that fed into those. So if you have a zillion tiny outputs and combine them into a few larger ones, subsequent transactions are not affected at all by the previous tiny outputs, and will be quite small.
Thanks, I'll stick to these guidelines when I send transactions from now on.
Update: 2014/05/25
The Monero team is happy to announce that we will be sponsoring development on the I2P project with a view to baking I2P support in to Monero!
Thanks for the great news! Do you have any reliable literature you (or anyone) would like to share regarding i2p and what it is/does? Wikipedia only goes so far, so I think it would be nice to see if you have anything educational (even technical is great) that you would like to share so what we can understand what this is?