These sites are primarily related to particle physics.  Many offer good web-based introductions to the theory and the experiments.
 

The Particle Adventure http://wwwpdg.cern.ch/pdg/particleadventure/index.html	This is the easiest to use version of an award-winning interactive web tour of particle physics.
Build an Atom with your Computer  http://www.pbs.org/wgbh/aso/tryit/atom/	Highly recommended. Comes with worksheet.
ALEPH events for Schools. http://iphlehramt.physik.uni-mainz.de/lehrsystem/	Interactive work using genuine ALEPH events.  In German.
Sub-Atomics: A guide to intelligent-sounding physics lingo!  http://members.aol.com/laninaia01/subatomics.html	An interesting (and well done!) qualitative summary of particle physics created by a student.
Particle Physics Introduction by Fermi Lab  http://www.fnal.gov/pub/hep_descript.html
Fermilab Education Office http://www-ed.fnal.gov/	Many links, on-line activities, and resources for educators
Education Programs and Resources http://www-ed.fnal.gov/talks/cern99/	This is the web-linked talk given to the CERN teachers by Liz Quigg of FermiLab.  Under web-based resources there are a number of son-line simulations at Fermilab and elsewhere.  Everything she spoke about is here.
An Introduction to Particle Physics  http://hepwww.rl.ac.uk/Pub/Phil/contents.html	A text-based introduction to particle physics from the Rutherford Lab (UK)
SLAC's Virtual Visitor Center http://www2.slac.stanford.edu/vvc/home.html	A very nice site with explanatory sections on the linear accelerator, particle physic theory, detectors, history and more.
Particle Physics in the UK http://hepweb.rl.ac.uk/ppUK/	Connected to CERN Outreach, a good jumpsite for particle physics, not only for the UK.  Includes resources for schools.
Boston University's ATLAS Education Website http://physics.bu.edu/ATLAS/index.html	An excellent site for introductions to particle physics, ATLAS, etc.  Includes wonderful EventMaker simulation of particle collisions.
A Multimedia Tour through Particle Physics  http://www.physik.uni-erlangen.de/didaktik/grundl_d_TPh/Titelseite.html	A nice site in German, with good pictures.
World Wide Web Interactive Real Event Display http://vanh.physto.se/~hoc/ (Stockholm mirror site)	Hands on CERN.Although still being perfected, this is a project we have been shown at CERN.  It allows students to analyze real detector data.  A CD-ROM is in the works.
Ba-Bar and the Missing Antimatter  http://www.compsoc.man.ac.uk/~heth/babar/index.html	Why is there more matter than antimatter? Easy to understand site on CP symmetry violation experiment.
Seeing particles  http://www.ep.ph.bham.ac.uk/user/watkins/seeweb/BubbleChamber.htm	Bubble chamber photographs and exercises for schools
Identifying events at LEP  http://hepwww.ph.man.ac.uk/~wyatt/events/home.html	Self guided tutorial for selected events at OPAL - with the answers!
All about neutrinos  http://wwwlapp.in2p3.fr/neutrinos/aneut.html	An informative guide to neutrinos.
Particles and the Universe http://www.iop.org/Schools/resources.html	.pdf file of an excellent article and lecture by Prof.Peter Kalmus.