6 Music and Asian Network, which have been threatened with closure by the BBC, have both won prizes at the Sony Radio Academy Awards.
Jarvis Cocker, who presents 6 Music's Sunday afternoon show, won the rising star award while the Adam and Joe Show won the best comedy title.
Radio 4 was the big winner with six prizes including a best breakfast show award for Today.
Johnny Vaughan's Capital FM breakfast show won best entertainment programme.
Radio 1's new music champion Zane Lowe scooped two awards, while Asian Network DJ Nihal took the best speech programme category.
5 live was named national station of the year and forces radio network BFBS won the special award.
Singer Cocker said: "6 Music is never going to be the biggest station in the UK but it would be devastating if it was to close.
"6 Music isn't going to change the world, it just wants to make it a bit nicer."
Picking up the award for the Adam and Joe Show, comedian Adam Buxton said: "My children went to school and boasted about the fact that their dad was on Radio 1 and knew Chris Moyles.
"When the children found out that wasn't true and, in fact, the station that dad was on was closing, it was very disappointing."
The BBC has proposed scrapping both 6 Music and the Asian Network in its strategic review.
The Today programme took the best breakfast show for a station with a potential 10 million-plus audience.
Other wins for Radio 4 included best music special for a poetic homage to Elvis by U2 singer Bono, best interview for Woman's Hour, and speech broadcaster of the year for wildlife expert Sir David Attenborough.
"Television, ladies and gentleman, is a doddle," said Sir David.
"If you have birds of paradise and gorillas, it's a doddle.
"Television is easy - radio terrifies me. I think it is extraordinarily difficult so my congratulations to you all who work in it."
In a strong night for the BBC, Radio 1's Scott Mills won music radio personality of the year, Zane Lowe won both music broadcaster of the year and the best specialist music prize, and Trevor Nelson won the Sony gold award for his outstanding contribution to radio.
Nelson said he was "really chuffed and really surprised".
"The music I've always championed has always been about R&B.
"When I first went on Radio 1 in 96, I said the words R&B and we got loads of complaints - 'that's not rhythm and blues, rhythm and blues is old 60s music'.
"I knew we were onto something because you get rid of the old guard, you bring in the new."
Radio 2's The Dermot O'Leary Show won best music programme while 5 live film critic Mark Kermode was named best specialist contributor.
The BBC World Service's Lyse Doucet won news journalist of the year.
Among the commercial station winners, Absolute scooped best competition, for The Christian O'Connell Breakfast Show, and live event coverage, for Blur at London's Hyde Park.
London's Kiss FM won the big local station of the year award while Planet Rock was named best digital station.
The Dixie and Gayle programme, on Real Radio Yorkshire, won the breakfast show prize for smaller stations.