Juniper has adopted a "best-of-breed" approach to networking. They have been a lot more selective in their acquisitions, and they have done a much better job of integrating what they did purchase into their product portfolios.
Along the security product lines, Juniper is arguably a much better solution for many, many features and functionality and performance. Their firewalls (NetScreen acquisition) blow away the PIX/ASA "comparables" from Cisco, the IPS technology (via acquisition from NetScreen/OneSecure) does an even better job of blowing away the Cisco equivalent (garbage), and their SSL VPN remote access technologies (via Neoteris/NetScreen) are untouchable. Cisco and Juniper do a more comparable job on IPSec VPN technology, but I would also argue that Juniper's policy-based VPNs are much better, too.
Juniper & Cisco's lines for application traffic management (and load balancing) are both not very good...stick with F5 for that.
The jury is still out on the WAN optimization comparison. Cisco may have a slight edge on this, only because they can drop this feature into a blade on a router. Juniper's appliances, though, deliver a ton more performance.
The routers are where it gets really interesting. Juniper's IP routing is exceptional. If you need routing of any other flavor (IPX, SNA, etc), Cisco is the only way to go. Most massive service providers run Juniper at the core because of the huge performance numbers and availability features. Over the past several years, Juniper has launched a new series of routers targeted at enterprises instead of service providers. They have the same features as the big ones, but aren't quite so massive. Pound-for-pound, they are usually less expensive than Cisco equivalents. Some major things in favor of Juniper routing:
1. SINGLE code train...this is huge. There are thousands of Cisco code/feature combinations. The same Juniper code applies to everything.
2. Separate control/forwarding planes. When under heavy load or attack, Juniper router configurations can be changed. Juniper has done this forever, and Cisco is now just catching on.
3. Modular operating systems. If an interface card on a Juniper router goes down or needs to be removed/replaced, only the operating system for that module needs to be rebooted...not the entire router's.
4. Juniper routers are built to support full performance will all features turned on. Add a ton of ACL's, turn on encryption & security, debugging, etc...and they will still run at near full rate. Do this on a Cisco box, and you'll need to buy something two sizes higher than what you really need.
In my experience, Cisco certifications are a dime-a-dozen now. They are still fully expected, but they do not differentiate one resume from another. Juniper-certified engineers, though, are commanding a lot more pay.
For most applications, I think Juniper is definitely the way to go.