Up to date list of QR Code management systems (also look in the comments section).
AzonMobile Sophisticated QR Code tracking and management system with an API (Application Program Interface) option.
Beqrious QR Code Tracking System
Dare2Scan Analytics PHP web application analyses QR Code traffic, mobile traffic from social networks, search engines, ad networks, SMS and Email. Available as a white label product.
Delivr Create QR Codes for URLs, Tweets, foursquare Check-ins, iPhone App Store Downloads, Android Market Downloads, Google Analytics Campaigns etc., in PNG, EPS, or SVG formats and track with activity maps.
Kishkee QR Code management and analytics, mobile site builder and mobile coupons. Free version and paid starting at $7.95/month
linkblots Mobile web pages and hosted mobile video and photo slideshows with mobile transcoding. There is a free option you can try with a monthly pageview/scans cap.
MyTAGG Includes a powerful mobile page editor with widgets system.
OpenQR QR Code based interactive marketing hub with advanced analytics management
QReate & Track Create QR Codes (one-at-a time or in bulk) and then track their effectiveness. There is a free option for creating codes only and a range of prices based on the number of QR Codes that you create and track each month.
QRinkle Analytics, Location Information, A/B Testing, Code Expiration and Bulk Code Import. Free account option.
QRme QR Code Campaign Management
QRmirror Free for personal and educational use
QRpro Signing up for an account is free and uses a pay per engagement (scan) pricing model
Qtag 14 day free trial
ScanLife 14 day free trial with prices starting at $50/month for small businesses.
SmartyTags Create, Track and Management with Cincinnati Zoo as one of their users. Free trial available.
TAGGINN Create and track QR Codes or Microsoft TAGs with comprehensive analytics. There is a free package available.
Ventipix QR Code Analytics & Campaign Manager