As an extremely long-toothed DM (basic set 'dice chits' anyone?), I'm reluctant to talk much about my homebrew system due to the inevitable discussion about what is broken in my rules or implications about what might be wrong with me. [here goes 'nothin'...]
A homebrew system I've used for years focuses deeply on the transition from mortal to divine, which turns out to be a very lengthy process (which could start at even very low levels). The HB kludges together the Birthright Campaign Setting (BRCS D20) rules to the Dicefreaks Deity Rules, offering a path to ascension. I won't post or share the rules because they are not fit for public consumption (written notes, etc), but I can summarize the system well for those interested in doing something similar.
Immortal Homebrew
Following the BRCS rules, mortals build their bloodline score to 40 through that system (rules available at link below), at which time they become a timeless outsider (the low end of immortal), and become Divine Rank (DR) 0 in name only, without most of the benefits defined for DR0 in the DDG.
The full benefits normally associated with DR0 are spread out over the next 20 levels of an Immortal prestige class, and to gain each level, a portion of the associated DR0 benefits, and an outsider HD, the PC/NPC must have a progressively higher BRCS bloodline score, which means they will either have to participate in blood theft (taking of others' bloodline power through slaughter or manipulation), or through further development of their domain ('domain' as defined in BRCS).
In the homebrew, levels in the Immortal PRC are called Immortal Ranks (ImR), akin to the Divine Rank system in the DDG. At ImR 20 (which happens to be bloodline score 100), the character finally attains full benefits of being Divine Rank 0 (quasi-deity), as defined in the DDG book.
I spread the benefits of DR0 over 20 levels because of the substantial ECL that would be associated with DR0 powers. Since DR0 itself doesn't represent an ECL of +20, the 20-level PRC progression also grants additional outsider HD and minor daily powers gained each level. Progressing through the 20-level PRC can be a challenge, with the requirement for continual progression in building the BRCS bloodline score.
ImR20 characters can petition a greater power to sponsor them into a pantheon at DR1 (if space "exists" in a pantheon), or alternatively might be able to ascend on their own if they can build their bloodline score to 120 (without further progression beyond ImR20).
On ascension from quasi-deity (DR0) to demigod (DR1), BRCS powers and bloodline score and ImR are shed and the character retains the 20 outsider HD (a feature common to DDG powers), chooses a portfolio and domain, is able to chose a new physical form, and undergoes a rebuild/retrain session. From that point forward, the mechanics for the character follow the Dicefreaks Deity Rules.
How you DM for PC gods is up to you. The Dicefreaks Deity Rules offer a balanced system, but that will likely be the least of your worries, as you'll be focused on preventing Armageddon (been there, done that.. boring!)
An afterthought... I can't emphasize enough that an immortal/divine campaign can quickly spin out of control as PCs gain power. A DM for such a campaign has to focus on role-playing vice roll-playing to ensure the campaign remains interesting and a challenge. Seek storyline rp opportunities. What does it mean to be timeless or to be a god? The benefits of immortality should be offset somehow with responsibility for the PCs (demanding followers, need to provide guidance and leadership, etc). Give nothing to the PCs for free, make them earn every bit of it, and they will be proud of what they have earned and will treasure the campaign. [edit-fix typo]
Birthright Campaign Setting (BRCS D20)
http://www.birthright.net/brwiki/index.php/BRCS:Main_Page
Dicefreaks Deity Rules
http://dicefreaks.superforums.org/viewtopic.php?f=14&t=19
I'm also a big fan of UpperKrust's Immortal's Handbook, which includes a Worship Point System where heroic deeds by mortals can result in ascension to divinity. While I haven't used UK's system in my game, I followed the (exhaustingly) long development process, have "pulled the legs" off his system, and believe it to be mechanically sound... and full of many inspiring concepts. Want epic level play? Set your ELH aside and pick up the IHB (Immortal's Handbook).
At one point, UK had conducted some deep forensics in calculating ECL. His research there was a great help in my effort to balance the 20 levels of my Immortal PRC. Hats-off and sweeping bow to UK, a god among men.
The Immortals Handbook
http://www.immortalshandbook.com/ascension.htm