A workaround used by some is to point the output location of a dependent project to be the classes folder of your web-project. The main issue with this approach is if you rebuild your web-project you need to rebuild all dependent projects also since the output area may be scrubbed (see Window>Preferences>Java>Compiler>Build Path>Scrub output… prefs).
Our initial idea since we didn’t support dependent projects for deployment was to treat web-projects in a manner similar to a JSP container. We know this is not good enough and are working to relax this ASAP as well as provide lots of other project structuring options. The idea we have is a concept of “deployable dependent project”. The main difference between this and tradtional dependent projects is that it will be deployed as part of a primary web-project deployment process. What we want to avoid is a case where ME will create a web-project that compiles but when deployed is missing classes from dependent projects; thus the current web-project restriction. I’m looking forward to 2.8 for this capability.