If you're 65 years old and made conversions from your standard IRA to Roth IRA in years 1999 $10,000, in 2000 $10,000 and in 2001 $10,000 a total of $30,000. This total amount appreciates to $45,000 in 2003 which is a 5 year waiting period since 1999.
Can the whole amount of $45,000 be withdrawn in 2003 without penalty? If not how much can be withdrawn in 2003?

The five year waiting period when the first Roth money went into the account in 1999 (it's a MORE THAN five year period) ends after 2003. If you convert $40K and take out $45K in 2003, you will be taxed on $5K. If you wait until 2004, nothing will be taxed. You will never pay a 10% penalty since you are over 59½.