It honestly depends on what your wants/needs are. I use Seeed regularly, and will continue to do so; they closed early for the Chinese New Year, and I used FlyPCB partly because I like to try new fab houses, and partly because I didn't want to wait until after the New Year holidays were over. (I also wanted to try them because I really like OSP as a PCB finish, and they're one of the few places that offer this, though not necessarily on prototypes. Neither Seeed, MakePCB, Golden Phoenix/BatchPCB, Sure Electronics' PCB service, or Olimex offer OSP finishing. Advanced Circuits does, but it's not a "standard" option, and thus excessively expensive, in that boards with OSP will never qualify for any kind of discount.)
Seeed offer very few options, other than solder-mask color, because they're just a middleman for some unspecified board house in China, and PCBs are just a small part of their business. For example, all they offer is HASL finishing - it's very nice HASL, some of the smoothest I've seen, though it may or may not be lead-free. Seeed's pricing is better only for the kind of prepackaged offers they have - when they offer it (they shutdown their PCB service early for the Chinese New Year) a comparable offer to the FlyPCB $40 offer would be ~$32.50, and you can actually get that down to ~$27.50 if you choose to skip electrical testing. Seeed insist on a minimum 8/8 trace/space, and a minimum 10mil hole size.
Seeed's "regular" fabrication is $50 + $0.12 per square centimeter.
On the other hand, FlyPCB offer all the options of a full-fledged fab house, because that's what they are. So, for people who like to use BatchPCB for prototypes, and then use Golden Phoenix for "production" boards, because they like knowing that WYSIWYG, FlyPCB is probably a very attractive alternative - get prototypes fabbed on 1.6mm 1oz green-soldermask HASL boards, fairly cheap, then have production boards made by the same company, only with, say, OSP finishing and black soldermask, on 2oz 2mm boards, or whatever. Their prototype service is 8/8 trace/space, the same as Seeed, but they'll do as low as 4/4, apparently.
FlyPCB's "quoted" prices are (for double-sided boards) $50 setup + $0.16 (or less) per square inch, and I suspect they might go slightly lower if you email them for a quote.
Like I said, I'll continue to use Seeed, particularly when I'm doing boards that involve very fine-pitch SMD semiconductors. (Their HASL is smooooooth.) They are - for what they offer - pretty much the cheapest place going, and their turnaround time is fairly decent, for an overseas fab house. They're not a fab house, though, so their ability to offer support is limited. FlyPCB, on the other hand, are very nice to deal with, know what they're doing, provide a very high-quality product, and offer substantially better pricing on production boards than Seeed... or Golden Phoenix, for that matter - and their basic boards are at least on par with GP, and probably better.
(Golden Phoenix offer 155 square inches of one design for $99, for 1oz 1.6mm FR4, HASL. Seeed would charge $175 or so for the same thing; FlyPCB would do it for about $75. Admittedly, Golden Phoenix would get it to you slightly faster, but if you're purely trying to find the cheapest place... Seeed isn't even close, and FlyPCB is 25% cheaper than GP. MakePCB, my current favorite for production PCB fabrication, would do it for +/-$5 of what FlyPCB charge - I make it out to be 56 Euros / $76, but the exchange rate varies - but the MakePCB boards would be gold-plated for that price.)
The "tl;dr" version: Both have their strengths and weaknesses. Seeed are cheaper for prototypes, and offer marginally higher-quality PCBs, albeit with no real options except soldermask color. FlyPCB are an actual board house with a lot of options, and offer significantly more attractive pricing than Seeed - or any of the other "usual suspects" - once you get to even small-volume / hobbyist production runs.
