clientlibs don't support versioning at the moment. but what speaks against having the version in the category-name?
if you want to share aspects of jquery with all versions, you can have the version specific jquery libraries extend:
e.g. my.jquery-1.3 depends on my.jquery.base.
My thought is that if I include the version in the name, then all sites using this component are required to use that version of jQuery, or load multiple versions. The idea of extending a base jQuery is interesting. I don't know enough about how jQuery handles their own versioning to say for sure, but I think I'll have to look into that.
ok, so you're saying that the same component should use a different jQuery version depending on the site it is operated under. you can achieve this by having a "site-configuration" that specifies the version of jQuery to use per site. you can store the version information as a content property, either directly or e.g. in design mode. you can then use that version info dynamically to include the correct client lib category, e.g in your JSP:
// get version from design with default = 1.3
String versionInfo = currentDesign.getStyle(resource).get("versionInfo", "1.3");
String clientlibCategory = "my.jquery-" + versionInfo;