The Special Edition also containes the longer Extended Version, but slightly altered again. The changes are so trivial your decision should not be influenced by them, but still, the SE is the prefferable version, simply because of the substantial bonus material and the high quality DVD.

The old DVD has been compared to the Special Edition DVD.

Theatrical Version DVD runtime: 1:48:36 Min. incl credits
Special Edition DVD runtime: 1:48:42 Min. incl credits
Added scenes: 3
Altered scenes: 1

DVD old version
1:14:34 Min.
Scott at the conference table with plans of the Enterprise.
0 Sec.

Special Edition
1:18:51 Min.
Different editing here.
0 Sec.

1:22:59 Min.
A close-up of unshaven Kirk has been added here.
0 Sec.

1:25:13 Min.
Spock does a spirit connection with Lietuenant Valeris. In the theatrical cut, the camera moves around them in a long scene. The special edition shows the picture of the respective traitor as his name is said, this is being emphasized by a short sound effect.

They are: Admiral Cartwright
0 Sec.

1:25:35 Min.
Christopher Plummer (as General Chang)
0 Sec.

1:25:55 Min.
And Ambassador Nanclus. (Connotation: After mentioning the Romulan's name, the theatrical version features the addition "and others!". This is now concealed by the sound effect described earlier.)
0 Sec.