So many choices! The Bob is big (duh) and surprisingly heterogenous in its terrain. Where you go ought to be determined by your preferences (high mountains, lakes, river valleys, forests) as well as where you'll be driving in from.
Richard's suggestion of doing a loop out of Holland Lake is a good one. Upper Holland Lake, Necklace Lakes, and Pendant Lake are lovely alpine ponds with great camping and views. You could do a loop down to the S Fork of the Flathead, down Burnt Creek and up Big Salmon Creek for instance, and see a good variety of terrain.
Another lovely loop, that I did last fall, starts at Monture Creek (in the southern Bob). Up over Falls Creek and Camp Pass, then down Canyon Creek to the Dry Fork of the Blackfoot. Up over the gentlest pass you'll ever find into the upper Danaher, then over Limestone Pass and down into Monture Creek and back to the TH. Spectacular hiking, and you get to spend a bit of time in valley, forest, and alpine in quick succesion. Great campsites throughout. Might be a bit shorter than 50 miles.
Of course, the Chinese Wall, Larch Hill, and My lake are justifiably famous. You can see our photos from that stretch (with lots of snow and no people!) in Le Parcour race report on this site. Doing a West Fork Sun River, Chinese Wall, Rock Creek loop from Gibson Reservoir would be nice. I'd also like to see that area by hiking up the Flathead to White River and White River Pass, then returning via Spotted bear.
You can't go wrong.
