It sort of depends upon what other lenses you have, if you need the macro to serve dual purpose.
The 100/2.8 non-IS is excellent and pretty much equal in image quality with the L/IS... I'd challenge anyone to tell apart images made with each of them. Both Canon 100s are very nice build quality, only people who haven't used them both would think one is better than the other. In fact, the 100/2.8 USM (non-L/IS) is identical build quality to L-series lenses, externally indistinguishable from the 180/3.5L, except for a stripe of red paint. The only reason the 100/2.8 USM wasn't an L is because it didn't need any exotic glass elements to do its job very, very well. Both the Canon 100s have all the bells and whistles (Internal Focusing, Focus Limiter, USM focus) including the ability to optionally fit a tripod mounting ring... which can be a very handy accessory for macro work. The 100L's Focus Limiter is slightly more sophisticated... three stage rather than the two stage of the 100/2.8 USM.
One difference... the 100/2.8 USM doesn't come with a lens hood, like most non-L series Canon lenses. It's another $45 or so to buy the matching hood, and it's huge! The 100L/IS comes with a hood, like most Canon L-series. Sort of off-setting the extra cost of the hood for the non-L, the tripod mounting ring for the L/IS is about $30 more expensive than the one for the non-L. However, there are third party clones of both available (look on eBay), for a lot less than the Canon OEM items.
Both the Canon 100s are fairly large for 100mm lenses. That's due to the Internal Focus, for the large part. The EF-S 60/2.8 is another excellent lens, a lot more compact and a bit less expensive. It's also got USM and is IF, but doesn't have a Focus Limiter and can't be fitted with a tripod ring (less necessary, since the lens is so much smaller). Some folks worry about the shorter focal length which also means shorter working distance, getting too close to the subject. That's true, but for flowers and a lot of larger insects, not really a problem. You're probably going to be shooting them at no more than half life size (1:2), so won't be all that close.
Michael mentions using for portraiture, too. Any of those Canons will do that too, though to be frank I'm not a big fan of using a macro lens for portraits. For one thing, they are only f2.8... there are times when a larger aperture is nice for portraits. Also, macro lenses are sharp... edge to edge. That's often not the best for portraits... not every subject is a 17 year old with perfect skin fresh from a $200 an hour make-up session. Finally, macro lenses in general are a bit slower focusing.... in part because they have to move their focusing group a long ways to go from infinity to 1:1, but also by design, "long throw focus" emphasizing accuracy over speed. Now, of the the three Canons mentioned above, the 60mm is the fastest, the 100L/IS is second, the 100/2.8 USM is the slowest. They are all okay for a lot of things, and for some portraits... but maybe not quick enough for candid shots, chasing kids or pet portraits. (The Canon 180/3.5L is a lot slower focusing, typical of longer macros.)
There are alternatives. I just got and am experiementing with the Tamron SP 60/2.0... it's unusual for a macro lens to have an f2 aperture, making it a bit more useful for portraits. Maybe it will replace my 50/1.4, 85/1.8 and other macro lenses in my camera bag. It's got really nice background blur, using 7-blade aperture that forms a near perfect circle because the blades are curved, much like some of Canon's top of the line lenses. I have been pleasantly surprised how fast focusing it is, because it doesn't have USM or a Focus Limiter. Nor can it be fitted with a tripod ring. But it's quite compact and - if it replaced three lenses - really lightens my load nicely.
But if you wanted a somewhat longer lens, 100mm fits into your camera and lens kit better, by all means either of the Canons would be a great choice. If you plan to use the lens a lot for non-macro shooting, the IS lens might be worthwhile. IS is most helpful at non-macro distances, though a 100mm lens is on the borderline of needing it, IMO. IS is less helpful at high magnifications, though the Canon's IS is more advanced and effective than stabilization other lens manufacturers have used.
Ultimately, only you can say if the IS is worth an extra $400 US, approx. To me, it's not. But it might be to you.