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I bought a new PC with Windows 7 preinstalled, and then I got a new SSD to freshly install OS on, and use the old hard drive as secondary. I didn't know much about the 200MB "System Partition" at the time.. and ended up just formatting that partition, giving it a drive letter, and resizing it, instead of deleting it.

Everything is working fine. That partition is now my "D:" drive and I have data on it. But in the partition manager, this partition still has a "System" label in the list of bits (Active, System, Primary, etc.).
Is there any harm in leaving it as a "System" partition, as long as I don't try to boot from it?
Is there any way I can remove this "bit" without wiping out the partition?

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You should be able to use SystemRescueCD and GParted to change flags of partitions without wiping them. (As always when using partitioning tools have a backup of your drive first.)

On the other hand if the computer is not behaving strangely there should be no harm in leaving the flag there. "If it ain't broken, don't fix it."

Edit: I've found references on the net that EasyBCD with it's dual booting support should be able to manage the system flag.

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Yes, I already experienced the "Fixing something that isn't broken" problem by removing the Active bit from the secondary hard drive, which made the whole machine unbootable :) Luckily that was an easy fix so I'm leaving that flag alone for sure. But I was just wondering if there was some obscure way that the System flag might cause a problem. –  Josh Aug 17 '12 at 14:13
I'm not aware of any problems that the system flag might cause. But on the other hand I'm a Mac user since 3 years so I'm not 100% updated. –  LapplandsCohan Aug 17 '12 at 14:23

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