The big killer is voltage drop over the cables - most USB devices just have a couple of diodes to drop to 3.3v internally, and if the voltage sags then you will start to see erratic operation.
Most that I've torn apart (and designed) have an LDO linear to go from the 4.5-5.5V Vbus down to a stable 3.3V. However, if you go below about 3.8-4V, the regulator will start to drop out (same result). I guess REALLY cheap USB devices may use diodes. Makes it harder to do proper soft-start (which most devices don't do anyway), though.
Note that the USB standard accounts for most of this. That's why Vbus can vary so much and why it has soft-start provisions. Unfortunately, everybody ignores all this stuff, violates the spec, then wonders why things don't always work right.
No motherboard I have seen has actually done anything with the power to the USB ports other then connect it straight to 5v, possibly via a PTC for some protection, but not proper current limiting.
Many laptops do enforce the limits. Many these days (especially small stuff like netbooks, tablets, and ultraportables) will enforce the actual allocated limit (i.e. if you draw more than you ask for, you'll get cut off), but some do just enforce a 500mA hard limit on every port. Sometimes that's done with a PTC, and sometimes it's done with an actual monitor/sense circuit which provides reliable error flag and on/off operation.
Most desktop motherboards I've seen create a dedicated "Vbus" rail that is connected to a 5V via a PTC that provides a limit at ~10% over max combined draw since it would be downright dangerous to connect Vbus directly to the 5V rail off the PSU (often capable of sourcing >25A!). So, if the mobo has 4 ports, there will be a ~2.25A PTC that attempts to protect the ports. Kinda a minimal protection if you ask me, but I guess it's cheaper than doing it the right way.
Some desktop motherboards support a "wake via USB" feature. These motherboards are capable of supplying Vbus via ATX +5VSB when in soft-off. Many of these mobos do enforce limits (at least a 500mA hard limit) since +5VSB has limited current capability (often 1A at best).
Of course, your LED-Wiz and similar have no idea how much power you're going to actually use. I would suspect those kind of devices just ask for the full 500mA. I'm guessing that's documented somewhere. If it does this, it may cause a failure to complete enumeration due to apparent lack of power unless you use a powered hub or plug it directly into your PC.
Bottom line: power your USB devices via USB like they are designed to be, and power your power loads (e.g. blinkenlichten) via a dedicated power line (from a suitable wall wart or your PC PSU). If you need more than 100mA per port on a 4-port (or larger) hub, make sure you use a powered hub. The power source for the hub is up to you: most come with a wall wart, and I'd recommend using it, but you could also run dedicated lines (I'd suggest 20AWG or larger) from your PC PSU if that fits your fancy better.
I would reccommend installing a 1A (or other suitable) fuse in your +5V source line for your power loads (blinkenlichten) for safety reasons. Large PC PSUs are capable of currents suitable for welding!