spider silk gfp fusion protein ("arachnicoli")
conversion of lactose into ethanol (Pavia 2009)
Using an AHL sensor (molecule secreted by biofilm microorganisms) and GFP reporter to detect biofilm formation in catheters (Imperial College London 2007)
Efficient pathway for the biosynthesis of bacteriochlorophyll
biological breathalyzer
melamine sensor
production of monoterpenes in Saccharomyces cerevisiae yeast by constructing biosynthetic pathways

Somewhat popularly well known projects

Salmonella typhimurium spider silk protein secretion
production of insulin
production of human growth hormone
clotting factors to treat haemophilia
biofuel stuff
blue rose (Florigene, Suntory)
plant (crop) tolerance to herbicides like glufosinate and glyphosate
plant (crop) tolerance or resistance to ringspot virus
plant (crop) production of bt toxin (an insecticide)
cassava with lower cyanogen glucosides and enhanced with protein and other nutrients
golden rice (to help fix Vitamin A deficiency)
vitamin-enriched variant of South African white corn
Camelina sativa oils
green fluorescent protein (GFP) modification of mice
ATryn, an anticoagulant that reduces blood clotting during surgery
- "On 6 February 2009, the U.S. Food and Drug Administration approved the first human biological drug produced from such an animal, a goat. The drug, ATryn, is an anticoagulant which reduces the probability of blood clots during surgery or childbirth. It is extracted from the goat's milk."
enviropig, a pig engineered to digest plant phosphorous
dairy cows to produce human breast milk (China, Argentina)
allergy-free dairy cow milk (New Zealand)
pig production of omega-3 fatty acids based on a roundworm gene
growth hormone for fish, see AquaBounty
malaria-resistant mosquitoes
GloFish (fluorescent zebra fish)
plant/crop with a gene from the winter flounder
Flavr Savr tomato, longer shelf life
ice-minus strain of P. syringae to protect crops from frost
virus-resistant tobacco in China (1992)
bromoxynil (a herbicide) resistant tobacco
insect resistant cotton (MON1445)
insect resistant maize (MON810)
herbicide tolerant soybean
miraculin (taste-modifying protein) in transgenic lettuce
mammalian expression of an infrared fluorescent protein
novel color vision in mice via transgenic expression of a photopigment protein
enlarged forebrains in mice via transgenic overexpression of beta-catenin
fluorescent sensors of cell membrane potential
MagA protein as a method of producing magnetic nanoparticles
recombinant monoclonal antibodies
crazy antibody stains
DNA vaccines

in processed food production

alpha-amylase from bacteria, which converts starch to simple sugars
chymosin from bacteria or fungi, which clots milk protein for cheese making
pectinesterase from fungi, which improves fruit juice clarity

crop stuff

Here is a better list: http://en.wikipedia.org/wiki/Genetically_modified_crops#Examples_of_genetically_modified_crops

just rna and dna

aptamers, for specifically binding to target molecules

DNA synthesis

One of the largest bottlenecks is DNA synthesis. Achieving $1/genome or lower costs of DNA synthesis would allow for many more projects. It seems unlikely that $1/genome or lower can be achieved with phosphoramidite synthesis.

Here are some related projects:

concepts

Some of these were originally from this email.

electronic control of polymerase
nucleotide gun made out of a nanotube pointed at the finger domain of some DNA polymerase
single-polymerase water droplet & add in a single dNTP at a time
physical display of dNTP as template for current base addition (i.e., on a stick) (not a protein template)
a protein that can undergo conformational changes that polymerase thinks represents the template strand
pull/push a template through DNA polymerase to control which dNTP it should be selecting for
protein-template DNA polymerase, where the polymerase itself has a giant protein that enzymatically encodes dNTP information (protein template, like in CCA-adding enzymes)
mechanical pressure on polymerase
some magical ultrasound method
replacing parts of traditional phosphoramidite synthesis with enzymes until the entire process is enzymatic
using multiple telomerase enzymes that you wash away after each step
light-dependent RNA tolermase also see this thread
a proposal for template-independent polymerases
enzymatic-mediated stepwise protein synthesis without DNA and without RNA
focus on tRNA synthetases as a method of enzymatic control over protein synthesis, then work backwards to DNA synthesis eventually
antibody-based selection mechanism?

Things that should be done

copying metabolic pathways from one species into a different species
genome synthesis of organisms/species that you don't physically have

Proteins

Here are some interesting proteins worth making in the event that you are able to make large proteins.

green fluorescent protein (GFP). These are especially useful for testing whether or not synthesis worked. Also, other biological pigments.

chromoproteins, like hemoglobin, myoglobin, cytochromes and flavoproteins.

blood clotting factor for hemophiliacs (see "Molecular approaches for improved clotting factors for hemophilia")

Enzymatic conversion of blood types, removal of blood type antigens

Various photoreceptors, including ultraviolet photoreceptors.

gelatin

Whatever protein makes magnetosomes in magnetotactic bacteria (maybe MamK).

MagA - for producing magnetic nanoparticles

type three secretion system is an "injectisome". "Structures similar to Type3SS injectisomes have been proposed to rivet gram negative bacterial outer and inner membranes to help release outer membrane vesicles targeted to deliver bacterial secretions to eukaryotic host or other target cells in vivo."

kinesin is a motor protein that drags cargo along microfilaments.

titin is a molecular spring used in human muscle, 3-4 nm in diameter and 1 micron long. See here.

hemoglobin, for oxygen transport.

"DAF-2 is an insulin receptor protein in worms and it has a similar function in humans. Worms without these proteins live twice as long as worms that have them." Maybe something that blocks DAF-2 receptors.

ATP synthase: a molecular rotor that synthesizes ATP. See video 1.

antibodies (maybe) (they have some other structure not including amino acids)

Akt1 - smooth muscle hypertrophy?

Various proteopathies may be fixable with protein synthesis

apoptosome - has an interesting shape

ferritin - stores and releases iron

transferrin - iron-binding blood plasma glycoproteins that control the level of free iron in biological fluids

phytosystems and chlorophyll - light-reactive

rhodopsin

chromophores

antifreeze proteins

enzymes/proteins useful for natural competence

enzymes needed for induced pluripotency in stem cells

luciferase

biotin

insect pheromones

channelrhodopsin - "Among the microbial opsins which can be used to investigate the function of neural systems are the channelrhodopsins (ChR2, ChR1, VChR1, and SFOs) to excite neurons. For silencing, halorhodopsin (NpHR),[23] enhanced halorhodopsins (eNpHR2.0 and eNpHR3.0),[24] archaerhodopsin (Arch), Leptosphaeria maculans fungal opsins (Mac), and enhanced bacteriorhodopsin (eBR) have been employed to inhibit neurons (see Figure 2), including in freely-moving mammals.[25]" see http://en.wikipedia.org/wiki/Optogenetics

functionalized bioplastics (like with gfp?)

various heat shock proteins

allophycocyanin - "Allophycocyanin (APC) is an intensely bright phycobiliprotein isolated from red algae that exhibits far-red fluorescence with high quantum yields. It is excited by laser lines at 594 and 633 nm, with an absorbance maximum at 650 nm and a fluorescence emission peak at 660 nm."

dye decolorizers

stomata-closing proteins in plants

theoretical proteins that would be nice to have

DNA capture compartment -- a giant organelle-like structure that absorbs and stores arbitrary dna it finds from the environment. Ideally, it would give some visual indication once it has absorbed at least one DNA molecule. Also, an RNA equivalent would be useful. It would be particularly useful if this sort of enzyme could be used prior to cleaning up ancient fossils (in case there really is DNA left around).

molecular lego with proteins based on binding affinity between lock and key domains, synthesize distinct proteins that lock together to form larger shapes and structures at the molecular level (molecular nanotechnology)

connectome sequencing (for brain scanning, brain uploading, synapse-level neuroanatomy, etc.)

Future iGEM project ideas

After reading all iGEM projects, here are some ideas for interesting future iGEM projects to pursue.

Surface display techniques: by introducing better and more varied surface display techniques, it becomes easier to do directed evolution and selection projects to optimize enzyme activity. Methods can be developed to focus on cleaving surface linkers, reversible surface linking, flagellar display (on the flagella itself), aptamer display and antibody display on surfaces, etc.
Directed evolution techniques focusing on secretion, surface display, exosomes, bacterial microcompartments, outer membrane vesicles (OMVs), etc.
TdT (terminal deoxyterminal transferase): Various enhancements to de novo DNA synthesis could be had by further investigation into TdT and other weird polymerases See http://2014.igem.org/Team:Cooper_Union/TdT_project and http://2015.igem.org/Team:Cooper_Union/DeNovoSynthesis for more details. In particular, there might be interesting directions to engineer mutant TdT enzymes, chimeric TdT enzymes, characterization of TdT activity, etc.
polymerases: In general, de novo DNA synthesis from polymerases would be highly useful in synthetic biology. "Weird properties" in polymerases, such as azobenzene amino acids to control polymerase, could be further explored.
Fusion proteins based on cas9 and recombinases for further genome editing techniques
Better than Gibson assembly? Characterization of homologous recombination pathways in ecoli and other bacteria. Optimization of homologous recombination from single pot many short 100mers. See https://groups.google.com/d/msg/enzymaticsynthesis/uyZqtJO24RE/lApLb4JmCAAJ for related ideas.
Genome sequencing of Rana sylvaticus (a frog): what are the antifreeze proteins and adaptations? Can these be used in other organisms?
Control and variation of morphological shape of microorganisms
embed DNA polymerase (or other DNA synthesizing molecules) in cell membranes such that DNA gets released immediately, do selection on length of produced DNA from these cells
DNA barcoding --- such as for lineage tracing, connectome sequencing, etc. Could probably get interesting results with recombinases and Cas9.
cryotoxin-resistant cells for various cryopreservation reagents (use directed selection techniques)
Human circadian rhythm sensor -- use dyes and pigments to report on human circadian clock status from urine samples or other samples
Directed evolution co-selection cultures -- use multiple bacteria to participate in selection by signalling and attacking underperforming cells in nearby media
More DNA assembly techniques: we can make 100mers but how do we make entire genomes from small fragments?
Simple demonstration of optogenetic stimulation to store information in a cell, and recombinases to load/read information from genetic memory to cause an optical response (probably coloration, dyes, etc). Could use signalling molecules to trigger the storage of information over time. DNA barcoding and DNA import through a pore could also be used to refer to specific regions of memory to elicit specific pre-programmed responses.
Simplified continuous directed evolution techniques (mRNA display is somewhat annoying at the bench)
magnetosome protein purification technique + cell-free freeze-dried protein transcription system and synthetic gene networks on paper -- could make for an interesting way to do protein production entirely without cells. Yields might still favor cell culture, though.
protein lego bricks -- binding by DNA addresses or other high affinity ligand specific techniques, for a stable toolbox of known protein structures and shapes and building up larger structures from small parts.