It depends on what you mean by "online" (Score 5, Insightful)

There are online courses, such as MIT's open courseware, and then there are online courses, such as UIUC's master of computer science. For courses that you take via Open Courseware, Kahn Academy or similar programs, I doubt your current or future employer will think much of it. For courses that you took towards a masters degree from an accredited brick-and-mortar university, on the other hand, should carry the same weight as if you attended them in person. Why? Because you are watching the same lecture that students physically present are watching.

I've been working towards my masters of science in computer science degree since 2007 (one class at a time takes forever). I started taking classes remotely at a remote television site at my employer. I later left that employer and got a job somewhere that didn't have access to those remote television sites, so I started taking the classes online. Since I started, I'm now at my third company, and all three have been more than willing to pay for my courses. In fact, that's probably the most telling point for whether anyone is going to take your courses seriously: is your company willing to pay for the classes. My advice is only take classes from a public or private university with a real physical campus, and only universities you would consider attending in person if you lived nearby.

Now, having taken courses remotely for several years, let me forewarn you about online learning:

• -- Online classes are harder than in-person classes. "But you said it's the same class that other students are taking in person!" Yup, it is. But those students have the ability to ask a question in lecture. They get to be in the room as it's happening and can look at all the boards the prof is using. When you watch it online, you watch what the video-taper thought was most important. I can't tell you the number of times I've been staring at a slide when the prof says something like "I'm pointing at the most important aspect of this class. If you don't understand this, you won't do well. Now this other thing, don't worry about that." "Wait!" I scream at my monitor. "What are you pointing at!"
• -- You get less attention than on-campus students. In the nine classes I've taken, I've had maybe 6 homeworks/exams returned to me. Most of those were from the same class. A guy I worked with got his MSEE from a California state school taking all courses online, and he always got his exams back, so it probably just depends on the university you attend.
• -- Some classes will still insist on group projects. Yup, group projects suck, but they suck even more when you have no way of meeting the other students in your class. Online students are also typically students that have other lives, which is why they are taking classes online! Coordinating your schedule with theirs is challenging, as is the process of vetting a good project partner.
• -- You may be required to physically show up to present a project. When I first started I had to take a prerequisite class that had a lab; a lab I had to drive 1 1/2 hours to attend in person, which wasn't so bad, but it would be three hours from where I live now. Take prerequisites from somewhere else if this isn't an option. My co-worker had to fly to California to take an exam. Both of these are the exception, not the rule, but be prepared for that possibility

Now going online also puts you in the driver's seat when it comes to choosing your institution. You get to pick from many more universities than are likely to be proximate to where you live. You can watch lectures multiple times, rewind to the part where the prof started speaking gibberish and watch it until you understand what the heck he's talking about. You can also choose a university where the courses are taught by professors and not TAs. I've had all of my classes taught by the professor. If you choose to pursue a degree either in person or online, good luck!