On this point, I strongly disagree.  When the "anti-spam" limit of 0.01 BTC was first put in to stop petty transactions, the value of 0.01 BTC was about a 20th of a cent.  That still allowed experimentation with microtransaction concepts with Bitcoins.... which now is mostly impossible.

The problem is that the protocol doesn't have any mechanism to adjust if the value of Bitcoins appreciates relative to other currencies, and I don't know of a reasonable way to make that happen either.

Right now, the "official client" that almost everybody has puts in a minimum transaction fee of 0.01 BTC if you attempt to send less than 0.01 BTC.  In effect, this is the absolute hard minimum transaction that can be sent using the reference implementation of the software.  Instead of being a trivial amount, that is now worth at least $0.01 dollars and is likely to go up.  Assuming the current rate of deflation of Bitcoins continues, that may soon be worth $0.10 dollars, and I can see that within a year or two as high as a dollar in value for 0.01 BTC.

This is a problem, and it could be a big one.  Yes, a patch can be done to solve this "problem" and alternate implementations of the software can be used to "solve" the issue too so it isn't as big of a deal as it would seem, but you can't use the current software to send those smaller amounts.  Miners may or may not accept these smaller transactions, but it is a client-side user interface issue and a presumption that shouldn't have been put into the client-side software in the first place.

The client user interface needs to have full control over transaction fees.... both for what that node will pay to initiate a transaction as well as what fees it will accept if it "wins" a block.  Burying this all in the source code on some high minded presumption of what you think the value of Bitcoins ought to be is pure bunk and something that ought not be there.  If somebody like lzsaver wants to refuse to deal with petty amounts less than 0.01 BTC when he is mining, that is his privilege... but it shouldn't be forced upon the community in an artificial manner as it is right now where this is the absolute minimum transaction which can take place.

Acceptance or rejection of a transaction belongs with the miners and I'm fine with that.  My issue is the presumptions put into the clients that are commonly spread throughout the community.  If it doesn't get changed, it will spawn a bunch of "alternative clients" that will put in the necessary changes.

Then again, that may be a good thing if the current reference implementation is simply abandoned.  If so, may it rest in peace, but that is a completely different topic here.  Giving developers a strong reason to fork Bitcoin could be useful.