Very Honorable Mentions...
I took the time to dig up these logos, so let's give them a look before we get into my top 50:
Standard: Standard bikes had a number of iconic graphics. The baseball font Standard always stuck out to me.
Lord Clothing: Lord has kept the upside-down cross logo for a long time and managed to make upsetting social situations fun for ages.
Peregrine: For a generation of riders in the later '80s to mid '90s, there was no better wheel than Peregrine Super Pro 48's. Their little falcon head font treatment logo is very recognizable.
Troy Lee Designs: Considering how much success this company has had and that its part of the the backbone of BMX history it probably should be higher. I just wasn't sure how to weigh that it wasn't specifically a BMX company with roots in MX as much as BMX.
Mutiny: I'm having a hard time adding newer companies to this list. I think Mutiny is going to make it through the test of time though and be a standout. Minimalist simplicity with a balance of design... or something. WTP, Subrosa, Shadow, Sunday, Orchid, and a bunch of others are all on my future list too.
RAD (movie): This logo is so godawful, but it really is iconic as it gets for BMX imagery. I'm probably just being jaded by not including it in the list.
Flite: With a logo screaming "MIami Vice," Flite pads had a good run on being cool for a while.