Cremona's project was about Rational points on conics. There is a description of the project, and some suggested readings for the project.
Cremona's web site has a number of preprints and and slides related to his talk at the Winter School, and to his student project. It also contains a lots of information about symbolic computation packages, other software, and mathematics.
Mazur's comments on the topic of visualizing elements in the Shafarevich-Tate group, (dvi, ps, pdf)
The paper Visualizing elements in the Shafarevich-Tate group, by Cremona and Mazur (to appear in the Journal of Experimental Math) (dvi, ps, pdf)
The paper Visualizing elements of order three in the Shafarevich-Tate group, by Mazur (to appear in the Journal of Asian Mathematics). (dvi, ps, pdf).
The Mazur student project led to a preprint by William Stein entitled Some Abelian Varieties with Visible Shafarevich-Tate Groups. (dvi, ps, pdf). Stein's web site also has many interesting tables, preprints, and program related to modular forms and modular Jacobians.
Pavlos Tzermias wrote up his Winter School Lectures as The Manin-Mumford Conjecture: A Brief Survey (dvi, ps, pdf)
Wetherell's project was on An application of the method of Coleman and Chabauty. Here is a description of the project; it refers to Wetherell's thesis, which is available in dvi, ps, and pdf formats.
Cathy O'Neil's thesis (dvi, ps, pdf) on Jacobians of Curves of Genus One was the basis of Tomas Klenke's talk.
Several U of A graduates students worked with Bill McCallum on constructing the Jacobian of a genus 1 curve. Their web site has the details. Slides for David Marshall's talk on this topic are available in dvi, ps, and pdf formats.
Poonen's lectures at the Winter School were on background material, but two (or more) of the papers on his web site are relelvant to the topic: Algebraic families of nonzero elements of Shafarevich-Tate groups (with Colliot-Thélène) (pdf), and Computational aspects of curves of genus at least 2 (ps, pdf)
Poonen's project was on The Mordell-Weil group of a genus 2 Jacobian. Here is a description of the project.