There are currently 3 models of the through-train to the "A"Levels in the Singapore education system.  This route is called the Integrated Programme. The route is a largely academic in focus and leads to the GCE "A" levels, and the students do not sit for the "O" Levels, unlike most of their peers in the conventional sec sch to JC route.

Model 1:
This is the through-train you get onto if you join the Raffles family or Hwa Chong family of schools. 

Entry mode:
through PSLE results or DSA in the pupil's P6 year
No. of years:
6 years from Sec 1 to Sec 4, followed by JC1-2
Final Exams:
"A" Levels
Start-point:
a) Sec 1 at Sec Raffles Girls' Sec or Raffles Institution leading to Raffles Junior College;
b) Sec 1 at Nanyang Girls' High Sch or Hwa Chong Institute (previously Chinese High Sch) and leading to or continuing in Hwa Chong Institute (previously also Hwa Chong Junior College)
This model represents ...
a merger of affiliates, leading independent secondary schools and their related Junior Colleges.
What has changed:
Entry for a sizeable number of students to these 2 top JCs is determined by PSLE T-scores and success in securing a place through the DSA in P6.
Gone are the days when one would see a full spectrum of school uniforms on the first day of JC1 in Hwa Chong Junior College (my JC) with some students reeling from the culture shock of being welcomed by unabashedly loud liondancers. 

Fees:
Independent sch fees, though by default Singaporeans who can get in may benefit from an Edusave Scholarship. Please consult the schools.

Model 2A:
Entry mode:
through PSLE results or DSA in the pupil's P6 year
No. of years:
6 years (akin to Sec 1 to Sec 4, followed by Yr 5-6)
Final Exams:
"A" Levels or International Baccalaureate.
Start-point:
Sec 1 at the following schools -
a) Anglo-Chinese Independent,
b) Dunman High Sch,
d) River Valley High Sch.
This model represents...
an extension of study in what was previously a leading secondary school,  and in a few schools a completely different though internationally recognised pre-university exam at the end of 6 years. 
What has changed:
The introduction of new pre-university exams in Singapore's Education landscape such as the IB.  There is no merger with any existing Junior College.  Entry is determined by PSLE T-scores and success in securing a place through the DSA as well as selection tests presently held from P6 Term 2 onwards.
Fees:
Independent or autonomous sch fees.  Please refer to the schools.

Model 2B
Entry mode: through PSLE results or DSA in the pupil's P6 year
No. of years: 6 years (akin to Sec 1 to Sec 4, followed by Yr 5-6)
Final Exams: NUS High Sch Diploma
Start-point: Sec 1 at the NUS High School of Mathematics and Science
This model represents specialisation in science and maths research and study.  NUS High was created to offer specialisation in science and maths and offer opportunities for early contact with NUS (National University of Singapore) academia.
What has changed: The introduction of a new pre-university exam, the NUS High School Diploma.  There is no merger with any existing Junior College.  Entry is determined by PSLE T-scores and success in securing a place through the DSA as well as selection tests presently held from P6 Term 2 onwards.
Fees: Please check with the school.

Model 3:
Entry mode:
Application in Sec 2, using one's PSLE results, Sec 1 year-end academic results, record of CCA involvement and student leadership since P5, referrals from teachers.  A General Ability Test ( like an IQ test) administered by the Civil Service College follows, then if you are shortlisted, an academic aptitude test (likely testing Maths and English) is the next hurdle.  Finally, if you survive the next cut, there is an interview.
No. of years:
4 years from what would have been one's Sec 3 year  to JC1-2
Final Exams:
"A" Levels
Start-point:
Sec 3 at the following Junior Colleges
a) National Junior College (in the NJC Integrated Programme)
b) Temasek Junior College (in Temasek Academy)
c) Victoria Junior College (in the Victoria Integrated Prog)
This model represents....
leading junior colleges admitting pupils in what would have been their Sec 3 year and preparing them for the "A" Levels eventually.  There are no affiliated secondary schools and no mergers with leading secondary schools.
What has changed:
Students who are successful have to transfer from their current secondary schools to these JCs.  Suddenly your P5 record of indulgent CCA involvement takes on a new relevance.
Fees:
Government sponsored fees typically but do check with the JC websites.

LATEST NEWS: in 2009, PSLE pupils will be able to apply for admission into National Junior College's New 6-year Integrated Programme from Secondary One.