Well, I think that when you capture a city, whether you get any 'beakers' towards your science-and how much-should depend on the answers to some of these questions:
1) Is the nation in question ahead of the capturing nation in any particular research streams (both in quantity of beakers invested AND # of techs ahead in said streams)? If not, then the capturing nation gains NO benefit whatever-in scientific terms-for the city capture.
2) What KIND of streams are they ahead in? Military, infrastructure and industrial techs should grant the greatest beaker 'capture', as they are easiest to 'reverse engineer', pure science, commerce and agriculture techs would produce the next best capture, the least one would be cultural and religious techs, as they are the most nebulous in nature.
3) How close is your culture group to theirs? The closer, the greater the beaker 'capture'.
4) How large is the city? The larger and more populous the city, the more beakers you can capture from it.
5) How 'long' was it between initiating hostilities against the city and actually capturing it? If you bomb a city with dozens of artillery before sending in your troops, then you should recieve fewer beakers from the capture, as the scientists and people have had ample time to 'destroy' much of the evidence of their high tech!
Hope that all made sense.
Yours,
Aussie_Lurker.