I'll have a go at a short list. This is more of a highlight and primer sort of response to a somewhat subjective question so pardon if this isn't what you wanted. I don't have paper references for all this, but I'll try to come back and add some later - I usually only have half an hour or so to write an answer so bear with me.
Synthetic biology as defined as the use of genes and promoters to engineer cells or even multicellular organisms like devices is a major category. I like browsing the projects from the iGem Competitions. A couple of outstanding efforts in this field are the use of photoreceptors to program E coli gene expression and the general effort to create logic and computational circuits in the cell.
A major application in systems biology is engineering cells to produce new chemical compounds or to overproduce compounds. A classic example (sort of old, but still pretty outstanding) is the engineering of E coli to produce the antimalarial drug artemisinin at levels which would enable world wide release of the drug. This has inspired efforts to produce fuel from algae and bacteria as well.
If you define Systems biology as being often concerned with modeling some or even all the biological processes of the cell, there are probably too many major efforts to cite, but this is just a list of some favorites.
There are lots of papers focused on flux balance analysis which models how the metabolic machinery processes and synthesizes all the scores of chemical compounds that make up a cell.
Another category of synbio tries to take the genes found in a genome and model the actions of all the genes. One of the most exciting papers to come out in this sort of systems biology is the whole cell model of Mycobacterium genetalium. Using data from a massive effort to characterize every gene in this very small genome, the model consists of over 20 specific models which have combined to make a very impressive simulation of the entire cell dividing.
Then there is metagenomics, which looks at the different populations of microorganisms and tries to look at how they vary with different environmental conditions. A recent paper that's exciting is the review of how different bacteria dominate in the gut of obese mice and people (several references in the link). A tour de force in metagenomics was the global sea survey.