If you read my post on the STL brown or the Black IPA you'll notice that whole hops annoy me. Pellet hops also annoy me, but for different reasons. There is no perfect solution to this problem.
The Problems with Hops:
Whole hops: clog my siphon, absorb lots of wort, float forever, but work better for dry hopping than pellets. Allegedly they impart less grassy-ness over time.
Pellet hops: will clog all manner of filters, are hard to remove from the wort, are difficult to clean when dried onto the inside of a better bottle, and can impart a grassy flavor when beer is over exposed to remnants of the pellets. They do have the upside of increased utilization.
(read more after the break)
Solutions Whole Hops:
Slotted spoons; I've used this one with my small batches to some success. I just use a slotted plastic spoon post chilling and press the whole mass of hops down to release trapped wort.
Hop Bags; Certainly easier to filter around; these have worked well for me. I end up ringing the bag out with my hands or pressing it with a sanitized spoon. I don't like to use my hands for sanitary reasons, and the spoon pressure method seems to work as well.
Brew pot filter (bazooka screen); this works well for filtering out whole hops from entering the ball valve, it worked great on my STL brown ale, but it did nothing to reclaim the wort lost to the hydration of the dried hops
Solutions Hop Pellets:
Hop Bags, the fine mesh bags do a good job of keeping the pellets contained, but I'm worried I am not getting as much surface area contact.
Filters, my funnel filter got clogged almost instantly and became useless. A filter with more surface area would work for longer but the fine particulate forms a firm barrier.
The best solution for hop pellets in the boil might be a large fine hop bag (or several) and just letting things happen. The water logged parts will settle out with the yeast, the floating parts will float, and you can siphon the beer from the middle.
Hop Bags make everything easier; allegedly they also lower your hop utilization(up to 10% claimed in various forums). Both hops types have their advantages and draw backs. I have been trying both trying to find a comfort zone with each type. The end game of this is probably that I'm going to have to make some Voile hop bags. I'll probably buy a yard of fabric and make as many as I can make.