You can't go into everyone's paper proceedings and add a yellow sticky to your paper saying to check out the new and improved journal version. But in this electronic age we can, in principle, add these notes.
First of all keep the papers on your webpage up to date. Many people just go to an author's page to download a paper and often they find some ancient version.
But after that then what? ECCC allows one to submit a revised version or add a comment which could point to a revised version. arXiv allows one to add journal information to an existing paper. Both of these require actions by authors that rarely happen. The digital libraries of proceedings publishers ACM and IEEE-CS don't have any mechanism to add pointers to later papers.
The field should have some standard mechanism for updating pointers to future papers. Until then we have to rely on the readers to find the latest papers on their own and perhaps hope that paper search tools like Citeseer, Google Scholar and Microsoft Academic Search will point to the latest and greatest version of a paper.