JGraphT worked alright in what I tried against in the past, but it won't
scale to huge heights like most libs without major tweaking or a graph DB
backing it along with some serious threading.

Just to throw in a few others I've used, but not with Smalltalk:
 
*  https://software.sandia.gov/trac/mtgl MTGL 
*  http://lemon.cs.elte.hu/trac/lemon LEMON 
* .NET  http://quickgraph.codeplex.com/ Quickgraph /Graph#
*  http://igraph.sourceforge.net/introduction.html iGraph 
*  http://snap-graph.sourceforge.net/ SNAP 

Of the above, I've had some of the best experience with LEMON in terms of
scale and speed for real-world usage. Unfortunately, none of these libraries
include everything you'd want, so at some point you will have to roll some
stuff yourself. That's been my experience at least.

Some Graph or Graph-like Databases (tend to have some algorithm libs as
well):

*  http://www.infinitegraph.com InfiniteGraph  (this runs on Objectivity
underneath the covers which has a Smalltalk impl)
*  http://www.neo4j.org neo4j 
*  http://www.kobrix.com/hgdb.jsp HyperGraphDB 

Some related useful items for dealing with large sets and graphs when you
are thinking about performance and/or parallel processing:

*  http://gauss.cs.ucsb.edu/~aydin/doc/html/index.html Combinatorial BLAS 
*  http://www.semanticdesigns.com/Products/PARLANSE/ PARLANSE 
*  http://research.microsoft.com/en-us/projects/dryadlinq/ DRYAD LINQ 

FYI, I would strongly recommend against using Ruby for anything with graphs
except as a simple client lib. I spent a lot of time on this before and it
simply does not scale or perform to anything beyond very simple cases, and
the memory footprint in a real app becomes horrendous. We had to tweak the
hell out of some libs to get anything decent and even then we ended up
writing stacks of C to compensate. If you're just dealing with 100 vertex
undirected graphs, then it works great. It's honestly the fault of a lot of
the libs rather than the language, but nonetheless be warned.
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