Which server works best with remote desktop 2003 or 2008 ?

2008 more better than2003

2008 is better, a new feature in Windows Server2008 R2 for the Remote Desktop Connection Broker (RD Connection Broker), formerly Terminal Services Session Broker, that will Allows users to reconnect to their existing sessions in a load-balanced RD Session Host server farm.
This also prevents a user with a disconnected session from being connected to a different RD Session Host server in the farm and starting a new session.
Enables you to evenly distribute the session load among RD Session Host servers in a load-balanced RD Session Host server farm.
and Provides users access to virtual desktops hosted on RD Virtualization Host servers and to RemoteApp programs hosted on RD Session Host servers through RemoteApp and Desktop Connection.

Oneof the Most Important Feature of Windows2008 is Remote Administration !

I worked on both 2003 and 2008, I noticed no significant changes in usability, I suggest going with 2008 since it comes with IIS 7.5 which has many more important built in features.
The most important in both cases to keep your Windows Updated for security issues.
Good Luck

I want more specific answer I know the answer, but there is a feature on server 2008 even if the employee income after it is running how to keeb server running with many session wihoute any session efects on any prosses on server ( your confgration mean)

ويندوز 2008 وr2 التقنية الجديدة لانظمة ميكروسوفت الخوادم وهي قفزة نوعية في مجال سيرفرات ميكروسوفت السهولة في الاستخدام والقابلية والحماية اللازمة والضرورية العالية عن ما كان سابقا في سيرفر 2003 معناه ان ويندوز 2008 اسرع من ويندوز 2003 والمواصفات العالية التي يتطلبها.

2008 will be better

2008 &2008R2 will be better option.