The colours do not have any specific meaning except that programs with similar purposes have generally been grouped together and given the same colour. The colours each have three shades to indicate the quality or confidence of the prediction. The colour shading may not come out very well on some browsers - sorry. Everything above this line is a feature found on the forward sense. Everything below it is a feature found on the reverse sense.
Some features are direction independent and so are duplicated on both strands.
The pretty blobs There are blocks and triangles and lines and arrows and blocks linked by lines and maybe a few other things. We may change what we use to display some features over time. Basically any one type of feature is displayed by the line or block or triangle etc. that we think looks best. The segmented blocks linked with lines are an attempt to link up distant regions that share some common property. This is most commonly used with blast matches and gene model predictions.