The following directory gathers a good many helpful online resources I have used or encountered during my research, and the links (not necessarily organized in accordance with strict taxonomy) are grouped as follows
Geometric Modeling
Computer Aided Geometric Design, Differential Geometry, Computational Geometry, Solid Modeling
Shape Representations
Mesh, Spline, Point, Subdivision, Implicit Surface
Artificial Intelligence
Maching Learning, Statistical Shape Modeling
Numerical Methods
Finite Element Method, Boundary Element Method, Isogeometric Analysis, Mathematical Optimization, Numerical Analysis
Computational Design/Manufacturing
Mechanics, Manufacturing, Shape Optimization, Topology Optimization
Software & Library
Data Sets

Geometric Modeling [Top]

Computer Aided Geometric Design
CAGD book - Farin
CAGD notes -Sederberg
Shape Interrogation for CADM (PDF)
Geometric Modeling notes
Solid Modeling
Geometric Modeling: A First Course
Geometric and Solid Modeling
Solid Modeling notes - Hoffmann
Solid Modeling notes - Shapiro
Solid Modeling notes - Sadimon
Introduction to Solid Modeling notes
Differential Geometry
Elementary DG - Raussen
Introduction to DG - Robbin
Comprehensive Introduction to DG - Spivak
DG course notes - Koch
Discrete DG forum (notes 1, notes 2)
Differential Geometry for CS course
Computational Geometry
Computational Geometry - d.Berg
Computational Geometry in C - O'Rourke (Code)
Graphics Gems (Code)
Discrete and Computational Geometry
Notes (Guibas, Mount, Shewchuck)
Geometry in Action portal
Computational Geometry Pages portal
Computational Geometry portal

Shape Representations [Top]

Polygon Mesh Processing
Mesh based Modeling @Eurographics
Elements of Geometry Processing (PDF)
Mesh parameterization course (PDF)
Mesh Deformation course (PDF)
Mesh & Grid Generation portal
Interative NURBS curve demo
Interactive Introduction to Splines demos
NURBS book (PDF)
Computing with Geometry notes
Geometric Modeling notes
Point-Based Graphics
Mark Pauly's thesis
Point-Based Computer Graphics notes
Point-Based Graphics portal
Subdivision Surface course (PDF)
Subdivision Methods (notes)
Subdivision course (Curves, Surfaces)
Subdivision notes (Curve, Surface)
Implicit Surface
Implicit Surfaces notes
Implicit Surfaces & Plolygonization notes
Implicit Surfaces notes
Introduction to Implicit Surfaces (notes)
Implicit surfaces notes

Artificial Intelligence [Top]

Maching Learning
Pattern Recognition & Machine Learning
The Elements of Statistical Learning (PDF)
Gaussian Processes for Machine Learning (PDF)
Information Theory, Inference & Learning Algorithms (PDF)
Machine Learning - Mitchell
Introduction to Machine Learning - Alpaydin
Introduction to Machine Learning - Smola
Machine Learning @VideoLectures
Deep Learning portal
Artificial Intelligence portal
Statistical Shape Modeling
Statistical Models of Shape - Davies
Statistical Shape Analysis - Dryden
Davies' thesis
Shape Symposium on SSM
Introduction to Active Shape Models - Cootes
Statistical Modeling Theory notes
A brief introduction notes
Geometry of Non-Rigid Shapes notes
In-the-Ear Hearing Aid Design thesis
SSM for geometry reconstruction thesis
Computing Correspondences @Eurographics

Numerical Methods [Top]

Finite Element Method
A First Course in Finite Elements
The Finite Element Method Set
Linear Static and Dynamic FEM
Courses (MIT, UMich, UColorado)
Notes (Papadopoulos, Liu)
Internet FEM portal
Boundary Element Method
BE: An Introductory Course
BEM with Programming
Symmetric Galerkin BEM
A Beginner's Course in BEM
Isogeometric Analysis
IGA textbook
ICES reports
IGA primer
IGA 2014
Mathematical Optimization
Introduction to Optimum Design
Numerical Optimization
Convex Optimization (PDF)
Linear & Nonlinear Programming (PDF)
Trust-Region Methods
Practical Optimization (Animations)
Optimization Online
Global Optimization portal
Numerical Analysis
Numerical Recipes(PDF)
Holistic Numerical Methods
Numerical Methods portal
Net Resources portal

Computational Design and Manufacturing [Top]

Applied Mechanics of Solids
Theory of Elasticity
Strength of Materials Vol. 1, Vol. 2
Introduction to Continuum Mechanics
Continuum Mechanics - Bower
Continuum Mechanics - McGinty
Additive Manufacturing Technologies
Principles of CAD/CAM/CAE
Manufacturing Engineering & Technology
Computer-Aided Manufacturingy
Shape Optimization
An Introduction to Structural Optimization
Shape Optimization And Optimal Designs
Shape Sensitivity Analysis
Principles of Optimal Design
Variational Methods in Shape Optimization
Structural Design Optimization
Topology Optimization
Topology Optimization
88 lines code
Topology Optimization Guide

Software & Library [Top]

OpenGL OpenGL.ORG, NeHe, Song Ho's, VideoLecturesRock, OpenGL-Tutorial, Nate Robins'
RedBook (Code), SuperBible, WikiBooks
Numerical MATLAB, Mathematica, Maple
PETSc, Eigen, Armadillo
FreeFEM, GetFEM; B-E-M, FastBEM; GeoPDEs, Igafem, PetIGA
3D/CAx NX, Catia, ProE, SolidWorks, AutoCAD, OnShape
COMSOL, SIMULIA, ANSYS, Nastran, HyperWorks, BEASY, Rhino3D, 3dsMax, Maya, Sketchup, Blender, Cinema4D
Mesh/Point Geomagic, VRMesh
MeshLab, OpenMesh, Gmesh, OpenFlipper, Graphite
Pointshop3D, PCL, CloudCompare
Image/Volume Mimics, OsiriX, 3DSlicer, 4DICOM
Development CGAL, LEDA, OpenCV, OpenSceneGraph
Visualization JT, VTK, Paraview, Tecplot, Geomview
GUI FLTK, wxWidgets, GTK, QT
Kernels Parasolid, ACIS, Open CASCADE, IntelliCAD, BRL-CAD, C3D, sgCore

Data Sets [Top]

Mesh Aim@Shape, Stanford, MIT (Deformation, Dynamic), GaTech, Princeton, Utah, Brown, Keenan's, CGV, Weise's, Washington, FastScan, UBC, LOD
Image CMU, CalTech, CAVIAR, USC, USF, Face-Rec, UMass
Volume Stanford, TU, Volvis, DigiMorph, Voreen, FAU, OSIRIX, Utah, UIowa, Aycan, Dicom info
Other UCI Repository, Damodaran's, KDnuggets

Miscellaneous [Top]

Mathamatics Multivariable Calculus, Paul's Notes, Bugman
Numerics IEEE754 Converter, Floating Point Arithmetic Primer
Geometry/Graphics Graphics Literature Portal, Real-Time Rendering, Volume Rendering, Computer Vision Compendium, Illuminations, Optical Illusions