Personalizing Online Assignments for a Statistics Class
The way you have worded your question it's not really clear why you have to mark the students' work online. Especially since you say that you generate assignments using sweave. If you use R to generate the (randomised) questions, then you really have to use R to mark them (or output the data set).
For my courses, I use a couple of strategies.

For the end of year exam (~500 students), each student gets a unique data set. The students log on to a simple web-site (we use blackboard since the University already has it set up). All students answer the same questions, but use their own unique data set. For example, "What is the mean". The answers are marked offline using an R script.
In my introductory R course, students upload their R functions and I run and mark them off line. I use sweave to generate a unique pdf for each student. Their pdf shows where they lost marks. For example, they didn't use the correct named arguments.

Coupling a simple web-form with marking offline gives you a lot of flexibility and is fairly straightforward.
I teach undergraduate statistics, and am interested in administering personalized online assignments. I have already solved one portion of the puzzle, the generation of multiple version of a question using latex/markdown + knitr/sweave, using seeds. 
I am now interested in developing a web-based system, that would use the various versions generated, and administer a different one for each student, online. I have looked into several sites related to forms (google docs, wufoo, formsite etc.), but none of them allow programmatic creation of questionnaires. 
I am tagging this with R since that is the language I am most familiar with, and is key to solving the first part of the problem. I know that there are several web-based frameworks for R, and was wondering whether any of them are suitable for this job.
I am not averse to solutions in other languages like Ruby, Python etc. But the key consideration is the ability to programatically deliver online assignments. I am aware of tools like WebWork, but they require the use of Perl and the interfaces are usually quite clunky. 
Feel free to add tags to the post, if you think I have missed a framework that would be more suitable.
EDIT. Let me make it clear by giving an example. Currently, if I want to administer an assignment online, I could simply create a Google Form, send the link to my students, and collect all responses in a spreadsheet, and automatically grade it. This works, if I just have one version of the assignment. 
My questions is, if I want to administer a different version of the assignment for each student, and collect their responses, how can I do that?