The 200 LEDs are driven by three transistors and one fixed 12v source
Determine what the likely Vce(sat) will be for those transistors at the current required, then take this into account as well.
What is your 12V supply? Is it a well regulated power supply (say a smps), or is it something that is unregulated and only nominally 12V?
, so I think I am going to have to break it down into:
Blue: (two transistors alternating 96 (48x2) LEDs @ 1Hz ) Vf: 3.2, I: 25mA. 2x(3x16) arrays with 2x(16) 100ohm resistors
Red: (50 flashing at about 2Hz from a transistor) Vf: 2, I: 25mA. 5x10 array with 82ohm resistors (is 82ohms too low?)
Green: (50 from a fixed 12v source) Vf: 3.2, I: 25mA. 3x16 array with 16 100ohm resistors
Those resistor values would be the smallest I would choose, and I would only consider them if the power supply was well regulated. I have not calculated the values required, I have assumed that you've done the math right, and they seem to be in the ballpark.
Thing is, these LEDs will be occupying a 8" by 8" square (ish) arranged into various patterns and such. This is going to be a lot more work then I bargained for ^_^
Using surface mount components would save you drilling 500 or so holes, but matrix board and point to point wiring would also work. You need to ensure that if you take a more free-form approach (like the latter) that you wire it up correctly.
Building something of this scale requires you to consider how you will power it up the first time. I would recommend you get a 1K, 100 ohm, 10 ohm, and 1 ohm resistor (of appropriate wattage) and first connect it up with the 1k resistor in series, do some reasonableness checks, before using the 100, 10, and 1 ohm resistors. If nothing untoward shows up (some LEDs surprisingly bright, current consumption more than expected, some LEDs not lit, etc.) then you can feel reasonably safe.
Remember that connecting a LED backwards can kill it in very short order. Be very careful with orientation and try to spot strings of LEDs that are not lit. If you're lucky, the reduced voltage, and the forward drop across the LEDs oriented correctly in a string may protect the one that's backwards.