Below I have sorted Seattle area biotechnology companies by technology classes. Viewing the companies this way helps to illustrate the various approaches being used to tackle different diseases:

Biologics (Peptides/Proteins)
Allozyne - Protein modification technology to make proteins
Arzeda - Uses computational approach to make novel enzymes
Calcionics - Peptide therapeutics targeting calcification
CMC ICOS Biologics - contract biologics manufacturing
Genzyme - Manufactures and sells Leukine in US, HQ in MA
Helix BioMedix - Bioactive peptides for skin disorders, infections
Implicit Bioscience - Small molecule dipeptides as anti-microbials
Novo Nordisk - Branch of Danish pharma focusing on immunity
ProFibrix - Drugs for hemostasis and regenerative medicine
Seredigm - Biological therapeutics for ischemia/reperfusion injury
Zymogenetics - Discovers and markets novel protein drugs

Gene Focused (Gene Therapy/Antisense/RNA Interference)
AVI Biopharma - RNA drug development in Corvalis, OR
MDRNA (formerly Nastech) - RNAi based company
Mirina - Uses microRNA to develop new drugs
Targeted Genetics - Gene therapy based drug company

Monoclonal Antibodies or Antibody Derivatives
Alder Biopharmaceuticals - Yeast monoclonals to treat diseases
Arrowsmith Technologies - Antibodies trap chemo for brain cancer
CisThera - Drugs for cancer, autoimmune disease, and others
North Coast Biologics - Rabbit high-affinity antibody based drugs
Seattle Genetics - Monoclonal antibodies for cancer treatment
Theraclone Sciences (was Spaltudaq) - Therapeutic antibodies
Trubion - Developing small modular immunopharmaceuticals
Xori - Making antibodies in chicken cells for faster, cheaper drugs

Modification of Existing Drugs/Drug Delivery Systems
Aequus BioPharma - Genetic polymer technology for biologics
Mediquest Therapeutics - Topical treatments for diseases
PharmIn - Copolymer drug delivery platform technology
PhaseRx - Multi-functional polymers to aid drug delivery
Scolr Pharma - Controlled drug delivery technology development

Small Molecules
Acucela - Drug therapies for blinding eye diseases
Aminex Therapeutics - Developing inhibitors of polyamine pathway
Amkor Pharma - Virtual biotech, clinical focus on neuroprotection
Artemisia BioMedical - Novel artemisinin-based therapeutics
Calistoga Pharmaceuticals - Developing PI3 kinase inhibitors
Cell Therapeutics Inc - Biologics and small molecules for cancer
Cocrystal Discovery - Small molecule anti-viral drugs
CompleGen - Functional genetics for drug discovery
Gilead - Lung disease discovery group in Seattle; HQ in CA
GPC-Rx - Developing G-protein coupled receptor based drugs
HemaQuest - Developing therapeutics for blood diseases
Icogenex - Drug discovery via high throughput proteomic screens
Ikaria - Focus on metabolic depression and critical care medicine
ISM Therapeutics - Therapeutics based on inositol signaling
Kineta - Small molecule drugs that enhance immunity
Koronis - Developing anti-viral drugs via viral decay methodologies
Light Sciences Oncology - Light activated oncology products
Obenomics - Small molecule approach to treating obesity
Oncogenex - Small molecule based oncology drug pipeline
Onkor Pharmaceuticals - Virtual company making cancer drugs
Pacific Northwest Biotechnology - Small molecule drug discovery
Poniard (was NeoRx) - Developing oncology products; HQ in CA
Promentix - Developing Alzheimer's disease therapies
ProteoTech - Small molecule development for amyloid diseases
Primal - Focus on G-protein coupled receptors
Qwell - Developing small molecule drugs from plant sources
Sound Pharmaceuticals - Drugs to prevent hearing loss
Syntrix Biosystems - Novel therapeutics and research platforms
VentiRx - Developing new small molecule drugs for cancer, ID

Small Molecules and Biologics
Amgen - Multi-national protein-based biotech headquartered in CA

Stem Cells
Cellcyte Genetics - Stem cell expansion bioreactor technology
Fate Therapeutics - Stem cell based therapies with HQ in CA
OncoMed Pharma - Therapies directed at cancer stem cells
Beat BioTherapeutics - Repair damaged hearts with stem cells

Vaccines (infectious Disease/Cancer)
CG Therapeutics - Anti-human chorionic gonadotropin vaccines
Dendreon - Vaccines for prostate cancer and other cancers
Etubics - Developing vector vaccines for infectious diseases
Immune Design - Developing therapeutics for infectious diseases
NW Biotherapeutics - Dendritic cell based cancer vaccines
Oncothyreon (formerly Biomira) - Oncology drugs and vaccines
TapImmune - Developing vaccines for oncology and infections

Virtual Companies (Minimal staff; most work contracted out)
Amkor Pharma - Virtual biotech, clinical focus on neuroprotection
HemaQuest - Developing therapeutics for blood diseases
Onkor Pharmaceuticals - Virtual company making cancer drugs

Not Able to Classify - Insufficient Technology Description
Ave Maria (AVM) Biotech - Working on ethical human therapeutics
Bio Architecture Lab - Spin off from David Baker's lab at the UW
ImaRxTherapeutics - Blood clot dissolving technology
Imdaptive - Profiles changes in the adaptive immune system
Omeros - Clinical stage company, focus on inflammation, CNS
Presage Therapeutics - Screen cancer drugs in vivo for efficacy
Procyte - Skin care products using copper peptide technology
Rasiris - Montana company developing breast cancer drugs
Recodagen - Targets mechanisms that allow cancer metastasis
Seattle Life Sciences - Zymogenetics spin-off in 2009
TherEpi Corporation - Epigenetic drug discovery focus
The Gene Pool, Inc - Molecular locks based drug discovery
Visient Therapeutics - Vision focused subsidiary of Light Sciences
VLST - Discovers new drug targets based on virus interactions