From an application developer's perspective, I tend to think of using SQLCLR as a violation of the three-tier model. The data tier really should be abstracted from the rest of the architecture. Some advantages of this abstraction are performance, scalability, and vendor-neutrality (MySQL? Anyone? Anyone?).

Additionally, I'm not now, nor even have been, a proponent of using the .Net framework, in *any* application tier. HTML, JavaScript, Ajax, and CSS have been my preferred technologies for the presentation and business logic tiers since .Net's initial release.