ISO 9001 vs ISO 13485
If you are in medical devices, use ISO 13485 (since it is required for EU and Canada, plus other countries recognizing it). There's no point in paying to maintain 2 certificates.
If you are not in device industry, then use ISO 9001, since ISO 13485 does not apply to you.
However, Contract Manufacturer for medical device products/components/sub-assemblies is a different story. Check with your customer(s) and find out what their expectations are from you. Usually they would prefer that their contract manufacturers are certified to ISO 13485, as we do with our contract manufacturers.
ISO 9001 requires continual improvement and customer satisfaction. Like Microsoft products, most device products that have software components usually have patches released later on to either fix something that was flawed in initial product release or enhance some functions/features that were there initially but weren't perfect. With this in mind, the customer satisfaction might be hard go gauge for device companies. All those software patches would lead one to speculate how effective (or rather how uneffective) was the design controls process, and that would open another can of worms (e.g. adequate assessment of customer requirements, adequate V&V activities, intended use and human factor issues, design transfer process, production & process controls, post-marketing activities, etc)...
In our case, we dropped ISO 9001:1994 and kept ISO 13485:1996 (plus CMDCAS) which we upgraded to ISO 13485:2003 (plus CMDCAS) this year. There were occasions that we got questioned about ISO 9001:2000; it just takes some time to explain the difference and applicability of the 2 standards to our industry. Everyone was satisfied with our explanations and our ISO 13485.