I second all of Gracia's suggestions. Satellite is a coffee shop--they have bagels with Tofutti or EB&nooch, and some other stuff (Vegan Treats, etc). If you're near south Philly, Benna's, B2 & Black & Brew all offer vegan breakfast options as well.
Soy Cafe: http://philadelphia.menupages.com/resta ... -cafe/menu
NoLibs. coffee, bagels, smoothies, salads & sandwiches
Grindcore House: http://www.grindcorehouse.com/
South Philly. 100% vegan. really great coffee, bagels (with a million different cream cheeses & toppings), sandwiches. plus a PPKer works there !
Satellite: http://www.yelp.com/biz/satellite-caf%C ... adelphia-2
West Philly. coffee, bagels, sandwiches
Fairmount (& Brewerytown & North Philly). fantastic coffee, bagels, sandwiches, 2 nondairy milks (almond & soy), some in-house vegan baked goods.
South Philly. both serve brunch (with at least 1 vegan option) every day starting at 11.
South Philly. B2 is the same thing basically/same owners. Smoothies, bagels, coffee, vegan soft serve.
Black & Brew: http://blackbrew.net/
South Philly. across the street from B2. Tofu scramble, usually at least one other vegan option. Bagels, coffee, sandwiches
Green Eggs: http://greeneggscafe.com/
NoLibs & South Philly (& according to their site, there is a 3rd in center city now). This place is a little nicer than all the aforementioned spots. Cash only! Amazing breakfast burrito, some other vegan options.
I'll continue with this list later. What neighborhood will you be in?