Due the relative unavailability or excessive cost of appropriate yellow and orange chips, other colors are often needed to be used in the T1000 slot when building a mixed tourney set from existing chips.
These are some of the 'alternate' colors that I think can be used for various tourney denominations without causing major confusion for experienced tournement players used to 'standard' colors (standard colors shown in parentheses):
T25 - blue (green)
T100 - grey, white, blue (black)
T500 - pink, red, blue, white, orange (purple)
T1000 - red, grey, white (yellow, orange)
T5000 - 'standard' colors include grey, pink, white, yellow, orange, and even blue. Pretty much anything goes here, pending the chosen colors for the other denoms.
One way to help a non-standard color denom chip gain immediate wider acceptance is to incorporate the 'standard' color as one of the spot colors (a white T500 with purple spots, or a grey T1000 with yellow spots, for example).
Typically, fewer T5000 and T500 chips are needed than the other denominations, and that can often make color selection decisions easier based on cost or availibility. Don't get too hung up on spot progression, either -- generally less important in tourney sets. Of greater practical use is ensuring that denominations don't get confused in stacks or pots, and avoiding using 'standard' tourney colors (green, black, purple) in non-standard places.
Don't overlook the potential advantages of a T2000 chip, either -- especially if yellow or orange chips are hard to come by (neither should be used as T2000). It's a great place to use a non-standard color, and can eliminate the need for both T1000 and T5000 chips.