what are the main differences between GNN and NN? Apart from GNN has
its input as a graph data?
Well, that is the main difference. Of course some corollaries of this fact is that GNNs can deal with variable sized graph inputs and typical NNs cannot, GNNs are not fully connected and typical (non-convolutional) NNs are, GNNs are usually invariant to permutation of the vertices and NNs are not.
In a bit more detail: Let $A$ be the adjacency matrix of some graph $G$, and let $X$ be an $n \times d$ matrix of features for each vertex, and let $W$ be a $d \times d'$ weight matrix. Then a graph neural network layer might compute something like $Y = \sigma(AXW)$. Inspired by spectral analysis, more sophisticated versions compute $Y = \sigma(\sum_i L^iXW_i)$ where $L^i$ is the $i$th power of the laplacian.
Just as in a convolutional network, the size of the weight matrix is independent of the graph -- you might interpret it as some sort of convolutional filter which can be slid over each vertex of the graph. Graphs with different sizes and connectivity simply alters $A$ and $L$, but not $W$.
Consequently, what is the potential in using GNN instead of NN, saying
for eg in knowledge graphs and bases?
Applications are very wide, and include...
Language models which operate on parse-trees rather than just a linear sequence of words. Improved Semantic Representations From Tree-Structured Long Short-Term Memory Networks
Solving reading comprehension by maintaining a graph of the relationships between all the different entities in a story. Learning Graphical State Transitions
Learning a model of physics by inferring the graph of physical interactions between objects. Neural Relational Inference for Interacting Systems and Interaction Networks for Learning about Objects, Relations and Physics
Improving segmentation boundaries Efficient Interactive Annotation of Segmentation Datasets with Polygon-RNN++
by modeling object boundaries as a graph.
A richer form of object detecion which not only detects objects in an image but reveals their relationship to each other. Graph R-CNN for Scene Graph Generation
Generating and predicting molecules with particular chemical properties. Junction Tree Variational Autoencoder for Molecular Graph Generation
Generating and learning patterns in real world road patterns. Neural Turtle Graphics for Modeling City Road Layouts
Since meshes are also graphs, you can generate / segment / reconstruct, etc. 3D shapes as well. Pixel2Mesh: Generating 3D Mesh Models from Single RGB Images Dynamic Graph CNN for Learning on Point Clouds
Neural networks are computation graphs, so you could use GNNs to learn to generate better network architectures. Graph HyperNetworks for Neural Architecture Search