(Initally imported from fiLi's world - The Top Universities in Taiwan (ROC))

According to the Institute of Higher Education of Shanghai Jiaotong University 2006  (World rank ; Asia rank) :

1. Natl Taiwan Univ (151-200 ; 20-24)
2. Natl Cheng Kung Univ (301-400 ; 41-63)
3. Natl Tsing Hua Univ (301-400 ; 41-63)
4. Natl Chiao Tung Univ (401-500 ; 64-92)
5. Natl Yang Ming Univ (401-500 ; 64-92)

-

According to Webometrics 2006 (World rank ; Asia rank) :

1. NATIONAL TAIWAN UNIVERSITY (159 ; 4)
2. NATIONAL CHIAO TUNG UNIVERSITY (305 ; 10)
3. NATIONAL CHENG KUNG UNIVERSITY (442 ; 20)
4. NATIONAL SUN YAT-SEN UNIVERSITY (470 ; 22)
5. NATIONAL TAIWAN NORMAL UNIVERSITY (547 ; 30)
6. NATIONAL TSING HUA UNIVERSITY TAIWAN (578 ; 32)

-

According to Times Higher Education Top 200 World Universities (World rank 2006 ; World Rank 2005) [use Bugmenot extension to login, or subscribe]:

1. National Taiwan University (108 ; 114)

(Yeah, NTU is the only one appearing in the top 200 universities list)

-

So, summing up, according to the world-rankings, NTU is high above all the others, while NCKU and NCTU are probably 2nd-3rd.