Really detailed write-up of how cells can be modeled and transformed with stochastic tie in http://www.eecs.berkeley.edu/~keutzer/classes/244fa2004/pdf/...
Parallel, stochastic, FGPA placement with great speedup http://www.eecg.utoronto.ca/~vaughn/papers/fccm2014_parallel...
Multi-optimization scheme for nanometer https://repositories.lib.utexas.edu/handle/2152/3688
Note: This does not do stochastic I don't think but a number of other methods. It's significant because it specifically mentions modern, typically large, designs avoid stochastic optimization for global issues because it's cost-prohibitive compared to geometric methods. That might have significant implications outside EDA, too. Might only be good for local optimizations that are tied together some other way.
Synthesis and control of system design for industrial project (software) http://www.scielo.org.ar/pdf/laar/v40n2/v40n2a07.pdf
RTL verification by minimizing multiway decision graphs (2006) http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=D9E...
Use in clock-tree synthesis for multi-FPGA's with focus on thermal properties http://thescipub.com/PDF/ajassp.2013.1604.1615.pdf
Synthesis of high-performance analog circuits (1996) https://users.ece.cmu.edu/~rutenbar/pdf/rutenbar-aotcad96.pd...
System levle hardware and software partitioning with simulated annealing and tabu search http://www.gstitt.ece.ufl.edu/courses/fall08/eel4930_5934/re...
Simulated annealing for aiding genetic algorithms in software architecture synthesis http://www.sis.uta.fi/~tp54752/pub/sa/SA_aiding_GA_acta.pdf
Synthesize implementations of hard real-time stuff http://link.springer.com/article/10.1007/BF00872288?no-acces...
Humie awards from Genetic Programming. Most of these could probably be ported to Stochastic Optimization in general. http://www.genetic-programming.org/combined.html
Accelerate floating point problems https://web.stanford.edu/~sharmar/pubs/fp.pdf
Stochastic super-optimization of loop-free binaries https://web.stanford.edu/~sharmar/pubs/asplos291-schkufza.pd...
Note: I'm keeping that one for sure. :)
But what I was specifically curious about was applications of stochastic optimization to EDA workflow. It sounded like you'd seen papers on that topic.
My interest is purely in applications of stochastic optimization. I'm not about to jump into EDA.