When the bars max out they start again in a different colour. And for every new colour each bar is more than the previous bar colour.
My bars haven't maxed out but you get the picture.
From memory don't the Ubuntu forums work similarly to this? In principle the idea is good but in practice someone just stumbling on the site would probably be a bit confused over who had less or more rep and what the colours were. Sure, they could look it up, but it's always nicer if they can be instantly and obviously compared like they are at the moment.
How about this along the same lines - leave the current green bar system as it is (though perhaps knock the max number of bars down to 10 and change the graphic to the nicer included one) but when people go beyond 1000 start replacing the green bars with stars, in the same format up to 2000. That way it's still fairly clear immediately (clearing than just using a different colour anyway) and no-one would lose any bars, they'd just get some stars if they had lots of rep already.
Beyond 2000 I really wouldn't bother too much, I mean there has to be some sort of a maximum and once you get that high you're clearly quite popular and reputable around these parts (and after all, isn't that what it's meant to show?) Perhaps use green stars initially and have them all change to gold or something similar when they reach something like 5000, but I personally wouldn't bother with anything incremental. To be honest, I'm not sure I'd bother with the stars changing colour bit at all (if it was me I'd probably just have them set to gold initially) but it's one option if you want something special to sort out the best from the best so to speak.
How does that sound?