Currently use of Solr or Lucene is not fully supported on Google App Engine, there are hacks around the issue but none seems perfect.
If I setup the Solr server via a cloud offering somewhere else, run the main site and application on GAE but use the Solr server for search functionalities, can anyone see any problems doing doing it this way?
The current (version 1.4.1) implementation of SolrJ (the Solr client for Java) doesn't work on GAE due to some external dependencies (mainly Apache Commons HTTP client). There are a few other gotchas, see this thread.
You can either contribute to the efforts towards a more portable SolrJ, or code directly against the Solr HTTP interface with the standard GAE HTTP client.